diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 3118 |
1 files changed, 1393 insertions, 1725 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index aad13317b8..8c3be14e65 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -265,21 +265,21 @@ structure of the predicted RNA.") `("PATH" ":" prefix (,path)) `("GUIX_PYTHONPATH" ":" prefix (,pythonpath))))))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("zlib" ,zlib) - ("python-nose" ,python2-nose) - ("python-pysam" ,python2-pysam))) - (inputs - `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+. - ("samtools" ,samtools) - ("bwa" ,bwa) - ("grep" ,grep) - ("sed" ,sed) - ("coreutils" ,coreutils))) + (list autoconf + automake + libtool + zlib + python2-nose + python2-pysam)) + (inputs + (list htslib-1.3 ; At least one test fails on htslib-1.4+. + samtools + bwa + grep + sed + coreutils)) (propagated-inputs - `(("python-numpy" ,python2-numpy))) + (list python2-numpy)) (home-page "https://ecogenomics.github.io/BamM/") (synopsis "Metagenomics-focused BAM file manipulator") (description @@ -314,7 +314,7 @@ instance, it implements several methods to assess contig-wise read coverage.") "-Wl,-rpath=" (assoc-ref outputs "out") "/lib/bamtools")) #t))))) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (home-page "https://github.com/pezmaster31/bamtools") (synopsis "C++ API and command-line toolkit for working with BAM data") (description @@ -350,7 +350,7 @@ BAM files.") (copy-recursively (assoc-ref inputs "libstatgen") "../libStatGen")))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs `(("libstatgen" ,(origin @@ -399,11 +399,9 @@ single executable called @code{bam}.") (("/bin/bash") (which "bash"))) #t))))) (native-inputs - `(("htslib" ,htslib) - ("perl" ,perl))) + (list htslib perl)) (inputs - `(("gsl" ,gsl) - ("zlib" ,zlib))) + (list gsl zlib)) (home-page "https://samtools.github.io/bcftools/") (synopsis "Utilities for variant calling and manipulating VCFs and BCFs") (description @@ -432,8 +430,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") #t)))) (build-system gnu-build-system) (native-inputs - `(("htslib" ,htslib-1.10) - ("perl" ,perl))))) + (list htslib-1.10 perl)))) (define-public bedops (package @@ -518,8 +515,7 @@ computational cluster.") (native-inputs `(("python" ,python-wrapper))) (inputs - `(("samtools" ,samtools) - ("zlib" ,zlib))) + (list samtools zlib)) (home-page "https://github.com/arq5x/bedtools2") (synopsis "Tools for genome analysis and arithmetic") (description @@ -567,8 +563,7 @@ BED, GFF/GTF, VCF.") (native-inputs `(("python" ,python-wrapper))) (inputs - `(("samtools" ,samtools) - ("zlib" ,zlib))))) + (list samtools zlib)))) (define-public pbcopper ;; This is the latest commit at the time of this writing. @@ -595,10 +590,9 @@ BED, GFF/GTF, VCF.") (substitute* "meson.build" (("-msse4.1") ""))))))) (inputs - `(("boost" ,boost))) + (list boost)) (native-inputs - `(("googletest" ,googletest) - ("pkg-config" ,pkg-config))) + (list googletest pkg-config)) (home-page "https://github.com/PacificBiosciences/pbcopper") (synopsis "Data structures, algorithms, and utilities for PacBio C++ applications") (description @@ -639,12 +633,9 @@ and utilities for PacBio C++ applications.") (string-append "'" (which "sh") "'")))))))) ;; These libraries are listed as "Required" in the pkg-config file. (propagated-inputs - `(("htslib" ,htslib) - ("pbcopper" ,pbcopper) - ("zlib" ,zlib))) + (list htslib pbcopper zlib)) (inputs - `(("boost" ,boost) - ("samtools" ,samtools))) + (list boost samtools)) (native-inputs `(("googletest" ,googletest) ("pkg-config" ,pkg-config) @@ -676,10 +667,9 @@ Non-PacBio BAMs will cause exceptions to be thrown.") "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd")))) (build-system gnu-build-system) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake))) + (list autoconf automake)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/nh13/pbgzip") (synopsis "Parallel Block GZIP") (description "This package implements parallel block gzip. For many @@ -741,14 +731,9 @@ libblasr_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n" #:tests? #f #:configure-flags '("-Dtests=false"))) (inputs - `(("boost" ,boost) - ("hdf5" ,hdf5) - ("htslib" ,htslib) - ("pbbam" ,pbbam) - ("zlib" ,zlib))) + (list boost hdf5 htslib pbbam zlib)) (native-inputs - `(("googletest" ,googletest) - ("pkg-config" ,pkg-config))) + (list googletest pkg-config)) (home-page "https://github.com/PacificBiosciences/blasr_libcpp") (synopsis "Library for analyzing PacBio genomic sequences") (description @@ -788,13 +773,9 @@ cpp.find_library('hdf5_cpp', dirs : '~a'), " #:tests? #f #:configure-flags '("-Dtests=false"))) (inputs - `(("boost" ,boost) - ("blasr-libcpp" ,blasr-libcpp) - ("hdf5" ,hdf5) - ("pbbam" ,pbbam) - ("zlib" ,zlib))) + (list boost blasr-libcpp hdf5 pbbam zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/PacificBiosciences/blasr") (synopsis "PacBio long read aligner") (description @@ -830,14 +811,14 @@ cpp.find_library('hdf5_cpp', dirs : '~a'), " "Ribotaper.sh"))) #t))))) (inputs - `(("bedtools" ,bedtools-2.18) - ("samtools" ,samtools-0.1) - ("r-minimal" ,r-minimal) - ("r-foreach" ,r-foreach) - ("r-xnomial" ,r-xnomial) - ("r-domc" ,r-domc) - ("r-multitaper" ,r-multitaper) - ("r-seqinr" ,r-seqinr))) + (list bedtools-2.18 + samtools-0.1 + r-minimal + r-foreach + r-xnomial + r-domc + r-multitaper + r-seqinr)) (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/") (synopsis "Define translated ORFs using ribosome profiling data") (description @@ -878,13 +859,10 @@ provides the Ribotaper pipeline.") (string-append line "\n" prefix "scripts=['scripts/TE.py'],\n")))))))) (inputs - `(("python-numpy" ,python2-numpy) - ("python-matplotlib" ,python2-matplotlib) - ("python-scipy" ,python2-scipy) - ("python-statsmodels" ,python2-statsmodels))) + (list python2-numpy python2-matplotlib python2-scipy + python2-statsmodels)) (native-inputs - `(("python-mock" ,python2-mock) - ("python-nose" ,python2-nose))) + (list python2-mock python2-nose)) (home-page "https://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") (synopsis "Detect translation efficiency changes from ribosome footprints") (description "RiboDiff is a statistical tool that detects the protein @@ -910,9 +888,9 @@ independently with transcriptional regulation.") "1pxc3zdnirxbf9a0az698hd8xdik7qkhypm7v6hn922x8y9qmspm")))) (build-system gnu-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("bison" ,bison))) + (list bison)) (arguments `(#:tests? #f ; There are no tests to run. ;; Bison must generate files, before other targets can build. @@ -951,11 +929,9 @@ intended to behave exactly the same as the original BWK awk.") "0ic07q85vhw9djf23k57b21my7i5xp400m8gfqgr5gcryqvdr0yk")))) (build-system python-build-system) (native-inputs - `(("python-setuptools-scm" ,python-setuptools-scm))) + (list python-setuptools-scm)) (propagated-inputs - `(("python-humanize" ,python-humanize) - ("python-requests" ,python-requests) - ("python-six" ,python-six))) + (list python-humanize python-requests python-six)) (home-page "https://pypi.org/project/htsget/") (synopsis "Python API and command line interface for the GA4GH htsget API") (description "This package is a client implementation of the GA4GH htsget @@ -1018,20 +994,17 @@ servers supporting the protocol.") (with-directory-excursion "/tmp/test" (invoke "pytest" "-v" "--doctest-modules"))))))) (propagated-inputs - `(("bedtools" ,bedtools) - ("samtools" ,samtools) - ("python-matplotlib" ,python-matplotlib) - ("python-pysam" ,python-pysam) - ("python-pyyaml" ,python-pyyaml))) - (native-inputs - `(("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-cython" ,python-cython) - ("kentutils" ,kentutils) ; for bedGraphToBigWig - ("python-six" ,python-six) - ;; For the test suite. - ("python-pytest" ,python-pytest) - ("python-psutil" ,python-psutil))) + (list bedtools samtools python-matplotlib python-pysam + python-pyyaml)) + (native-inputs + (list python-numpy + python-pandas + python-cython + kentutils ; for bedGraphToBigWig + python-six + ;; For the test suite. + python-pytest + python-psutil)) (home-page "https://pythonhosted.org/pybedtools/") (synopsis "Python wrapper for BEDtools programs") (description @@ -1046,8 +1019,8 @@ Python.") (package (inherit pybedtools) (native-inputs - `(("python2-pathlib" ,python2-pathlib) - ,@(package-native-inputs pybedtools)))))) + (modify-inputs (package-native-inputs pybedtools) + (prepend python2-pathlib)))))) (define-public python-biom-format (package @@ -1098,19 +1071,16 @@ Python.") (for-each (lambda (file) (chmod file #o644)) (find-files out "\\.gz")))))))) (propagated-inputs - `(("python-anndata" ,python-anndata) - ("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-flake8" ,python-flake8) - ("python-future" ,python-future) - ("python-click" ,python-click) - ("python-h5py" ,python-h5py) - ("python-pandas" ,python-pandas))) - (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-nose" ,python-nose))) + (list python-anndata + python-numpy + python-scipy + python-flake8 + python-future + python-click + python-h5py + python-pandas)) + (native-inputs + (list python-cython python-pytest python-pytest-cov python-nose)) (home-page "http://www.biom-format.org") (synopsis "Biological Observation Matrix (BIOM) format utilities") (description @@ -1149,17 +1119,15 @@ e.g. microbiome samples, genomes, metagenomes.") (with-directory-excursion "/tmp" (invoke "pytest" "-v"))))))) (native-inputs - `(("python-cython" ,python-cython) - ("python-nose" ,python-nose) - ("python-pytest" ,python-pytest))) + (list python-cython python-nose python-pytest)) (inputs `(("python" ,python-wrapper))) (propagated-inputs - `(("htslib" ,htslib) ; for bgzip, looked up in PATH - ("samtools" ,samtools) ; looked up in PATH - ("lz4" ,lz4) ; for lz4c - ("python-click" ,python-click) - ("python-numpy" ,python-numpy))) + (list htslib ; for bgzip, looked up in PATH + samtools ; looked up in PATH + lz4 ; for lz4c + python-click + python-numpy)) (home-page "https://github.com/mirnylab/pairtools") (synopsis "Process mapped Hi-C data") (description "Pairtools is a simple and fast command-line framework to @@ -1226,12 +1194,9 @@ alignments and perform the following operations: (find-files bin "\\.pl$")) #t))))))) (inputs - `(("perl-module-build" ,perl-module-build) - ("perl-data-stag" ,perl-data-stag) - ("perl-libwww" ,perl-libwww) - ("perl-uri" ,perl-uri))) + (list perl-module-build perl-data-stag perl-libwww perl-uri)) (native-inputs - `(("perl-test-most" ,perl-test-most))) + (list perl-test-most)) (home-page "https://metacpan.org/release/BioPerl") (synopsis "Bioinformatics toolkit") (description @@ -1259,11 +1224,9 @@ provide a coordinated and extensible framework to do computational biology.") "0hjg0igfkpvh27zdkdr6pa7cqm9n6r7cwz0np74cl4wmawgvr9hj")))) (build-system perl-build-system) (native-inputs - `(("perl-module-build" ,perl-module-build) - ("pkg-config" ,pkg-config))) + (list perl-module-build pkg-config)) (propagated-inputs - `(("bioperl-minimal" ,bioperl-minimal) - ("htslib" ,htslib-1.9))) + (list bioperl-minimal htslib-1.9)) (home-page "https://metacpan.org/release/Bio-DB-HTS") (synopsis "Perl interface to HTS library for DNA sequencing") (description "This is a Perl interface to the HTS library for DNA @@ -1289,7 +1252,7 @@ sequencing.") ;; Some tests require a home directory to be set. (lambda _ (setenv "HOME" "/tmp") #t))))) (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (home-page "https://biopython.org/") (synopsis "Tools for biological computation in Python") (description @@ -1363,7 +1326,7 @@ relying on a complex dependency tree.") (when tests? (invoke "./bin/biosoup_test"))))))) (native-inputs - `(("googletest" ,googletest))) + (list googletest)) (home-page "https://github.com/rvaser/biosoup") (synopsis "C++ support library for bioinformatics tools") (description "Biosoup is a C++ collection of header-only data structures @@ -1394,11 +1357,11 @@ used for storage and logging in bioinformatics tools.") (when tests? (invoke "./bin/bioparser_test"))))))) (inputs - `(("biosoup" ,biosoup))) + (list biosoup)) (propagated-inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("googletest" ,googletest))) + (list googletest)) (home-page "https://github.com/rvaser/bioparser") (synopsis "C++ library for parsing several formats in bioinformatics") (description "Bioparser is a C++ header only parsing library for several @@ -1448,12 +1411,9 @@ compressed files.") ("rust-serde" ,rust-serde-1) ("rust-seq-io" ,rust-seq-io-0.3)))) (inputs - `(("bioparser" ,bioparser) - ("biosoup" ,biosoup))) + (list bioparser biosoup)) (native-inputs - `(("cmake" ,cmake) - ("pkg-config" ,pkg-config) - ("googletest" ,googletest))) + (list cmake pkg-config googletest)) (home-page "https://github.com/Kevinzjy/circtools") (synopsis "Accelerating functions in CIRI toolkit") (description "This package provides accelerated functions for the CIRI @@ -1501,21 +1461,19 @@ consensus sequences.") (substitute* "CIRI_long/main.py" (("os.chmod\\(lib_path.*") ""))))))) (inputs - `(("circtools" ,circtools) - ("python-biopython" ,python-biopython) - ("python-bwapy" ,python-bwapy) - ("python-levenshtein" ,python-levenshtein) - ("python-mappy" ,python-mappy) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pysam" ,python-pysam) - ("python-pyspoa" ,python-pyspoa) - ("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy))) - (native-inputs - `(("python-cython" ,python-cython) - ("python-nose" ,python-nose) - ("python-setuptools" ,python-setuptools))) + (list circtools + python-biopython + python-bwapy + python-levenshtein + python-mappy + python-numpy + python-pandas + python-pysam + python-pyspoa + python-scikit-learn + python-scipy)) + (native-inputs + (list python-cython python-nose python-setuptools)) (home-page "https://ciri-cookbook.readthedocs.io/") (synopsis "Circular RNA identification for Nanopore sequencing") (description "CIRI-long is a package for circular RNA identification using @@ -1583,14 +1541,14 @@ $(BOOST_LIB)/libboost_program_options.so")))) (mkdir-p bin) (install-file "bin/QTLtools" bin))))))) (inputs - `(("curl" ,curl) - ("gsl" ,gsl) - ("boost" ,boost) - ("rmath-standalone" ,rmath-standalone) - ("htslib" ,htslib-1.3) - ("openssl" ,openssl) - ("openblas" ,openblas) - ("zlib" ,zlib))) + (list curl + gsl + boost + rmath-standalone + htslib-1.3 + openssl + openblas + zlib)) (home-page "https://qtltools.github.io/qtltools/") (synopsis "Tool set for molecular QTL discovery and analysis") (description "QTLtools is a tool set for molecular QTL discovery @@ -1653,8 +1611,7 @@ providing them a set of re-usable tools.") ;; so the tests fail. #:out-of-source? #f)) (inputs - `(("bpp-core" ,bpp-core) - ("bpp-seq" ,bpp-seq))) + (list bpp-core bpp-seq)) (home-page "http://biopp.univ-montp2.fr") (synopsis "Bio++ phylogenetic Library") (description @@ -1685,8 +1642,7 @@ library provides phylogenetics-related modules.") `(#:parallel-build? #f #:tests? #f)) ; There are no tests. (inputs - `(("bpp-core" ,bpp-core) - ("bpp-seq" ,bpp-seq))) + (list bpp-core bpp-seq)) (home-page "http://biopp.univ-montp2.fr") (synopsis "Bio++ population genetics library") (description @@ -1719,7 +1675,7 @@ library provides population genetics-related modules.") ;; so the tests fail. #:out-of-source? #f)) (inputs - `(("bpp-core" ,bpp-core))) + (list bpp-core)) (home-page "http://biopp.univ-montp2.fr") (synopsis "Bio++ sequence library") (description @@ -1750,9 +1706,7 @@ library provides sequence-related modules.") `(#:parallel-build? #f #:tests? #f)) ; There are no tests. (native-inputs - `(("groff" ,groff) - ("man-db" ,man-db) - ("texinfo" ,texinfo))) + (list groff man-db texinfo)) (inputs `(("bpp-core" ,bpp-core) ("bpp-seq" ,bpp-seq) @@ -1891,7 +1845,7 @@ package provides command line tools using the Bio++ library.") ("perl" ,perl) ("python" ,python-wrapper))) (native-inputs - `(("cpio" ,cpio))) + (list cpio)) (home-page "https://blast.ncbi.nlm.nih.gov") (synopsis "Basic local alignment search tool") (description @@ -1977,13 +1931,9 @@ confidence to have in an alignment.") '("bless" "kmc/bin/kmc"))))) (delete 'configure)))) (native-inputs - `(("perl" ,perl))) + (list perl)) (inputs - `(("openmpi" ,openmpi) - ("boost" ,boost) - ("sparsehash" ,sparsehash) - ("pigz" ,pigz) - ("zlib" ,zlib))) + (list openmpi boost sparsehash pigz zlib)) (supported-systems '("x86_64-linux")) (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/") (synopsis "Bloom-filter-based error correction tool for NGS reads") @@ -2042,10 +1992,7 @@ errors at the end of reads.") ("zlib" ,zlib) ("python" ,python-wrapper))) (native-inputs - `(("perl" ,perl) - ("perl-clone" ,perl-clone) - ("perl-test-deep" ,perl-test-deep) - ("perl-test-simple" ,perl-test-simple))) + (list perl perl-clone perl-test-deep perl-test-simple)) (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") (synopsis "Fast and sensitive nucleotide sequence read aligner") (description @@ -2086,9 +2033,7 @@ gapped, local, and paired-end alignment modes.") (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("python-wrapper" ,python-wrapper) - ("tbb" ,tbb-2020) - ("zlib" ,zlib))) + (list python-wrapper tbb-2020 zlib)) (supported-systems '("x86_64-linux")) (home-page "http://bowtie-bio.sourceforge.net/index.shtml") (synopsis "Fast aligner for short nucleotide sequence reads") @@ -2210,7 +2155,7 @@ splice junctions between exons.") (install-file "bwa.1" man)))) ;; no "configure" script (delete 'configure)))) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) ;; Non-portable SSE instructions are used so building fails on platforms ;; other than x86_64. (supported-systems '("x86_64-linux")) @@ -2251,9 +2196,7 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for (substitute* "pssm.c" (("inline int map") "int map")))))))) (inputs - `(("gdsl" ,gdsl) - ("zlib" ,zlib) - ("perl" ,perl))) + (list gdsl zlib perl)) (home-page "http://bwa-pssm.binf.ku.dk/") (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper") (description @@ -2292,9 +2235,9 @@ well as many of the command line options.") (("^checkX.*") "")) #t))))) (inputs - `(("bwa" ,bwa))) + (list bwa)) (native-inputs - `(("python-toolshed" ,python-toolshed))) + (list python-toolshed)) (home-page "https://github.com/brentp/bwa-meth") (synopsis "Fast and accurante alignment of BS-Seq reads") (description @@ -2322,13 +2265,11 @@ off-target reads for a capture method that targets CpG-rich region.") "0mclahslz34vq9x424jmzsxk0nmpm1j716fa8h3zwr9ssvch7skc")))) (build-system python-build-system) (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("python-lzo" ,python-lzo) - ("python-nose" ,python-nose) - ("python-cython" ,python-cython))) + (list python-lzo python-nose python-cython)) (home-page "https://github.com/bxlab/bx-python") (synopsis "Tools for manipulating biological data") (description @@ -2350,13 +2291,9 @@ multiple sequence alignments.") (arguments `(#:tests? #f)) ; The tests require network access. (native-inputs - `(("python-psutil" ,python-psutil) - ("python-htsget" ,python-htsget))) + (list python-psutil python-htsget)) (propagated-inputs - `(("python-requests" ,python-requests) - ("python-tqdm" ,python-tqdm) - ("python-urllib3" ,python-urllib3) - ("python-responses" ,python-responses))) + (list python-requests python-tqdm python-urllib3 python-responses)) (home-page "https://github.com/EGA-archive/ega-download-client") (synopsis "Python client for EGA") (description "This package is a python-based tool for viewing and @@ -2428,18 +2365,16 @@ has several key features: " and not TestHeaderCRAM" " and not test_text_processing"))))))))) (propagated-inputs - `(("htslib" ,htslib-1.10))) ; Included from installed header files. + (list htslib-1.10)) ; Included from installed header files. (inputs - `(("ncurses" ,ncurses) - ("curl" ,curl) - ("zlib" ,zlib))) + (list ncurses curl zlib)) (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ;; Dependencies below are are for tests only. - ("samtools" ,samtools-1.10) - ("bcftools" ,bcftools-1.10) - ("python-nose" ,python-nose))) + (list python-cython + python-pytest + ;; Dependencies below are are for tests only. + samtools-1.10 + bcftools-1.10 + python-nose)) (home-page "https://github.com/pysam-developers/pysam") (synopsis "Python bindings to the SAMtools C API") (description @@ -2468,7 +2403,7 @@ also includes an interface for tabix.") ;; Tests are not included (arguments '(#:tests? #f)) (native-inputs - `(("python-sphinx" ,python-sphinx))) + (list python-sphinx)) (home-page "https://github.com/benjschiller/twobitreader") (synopsis "Python library for reading .2bit files") (description @@ -2491,17 +2426,16 @@ UCSC genome browser.") ;; Some test files are not included. `(#:tests? #f)) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-pandas" ,python-pandas) - ("python-pysam" ,python-pysam) - ("python-matplotlib" ,python-matplotlib) - ("python-biopython" ,python-biopython) - ("python-twobitreader" ,python-twobitreader) - ("python-termcolor" ,python-termcolor))) - (native-inputs - `(("python-cython" ,python-cython) - ("python-nose" ,python-nose))) + (list python-numpy + python-scipy + python-pandas + python-pysam + python-matplotlib + python-biopython + python-twobitreader + python-termcolor)) + (native-inputs + (list python-cython python-nose)) (home-page "https://github.com/joshuagryphon/plastid") (synopsis "Python library for genomic analysis") (description @@ -2558,12 +2492,12 @@ high-throughput sequencing data – with an emphasis on simplicity.") "TEcount"))) #t))))) (inputs - `(("coreutils" ,coreutils) - ("bedtools" ,bedtools) - ("python-argparse" ,python2-argparse) - ("python-pysam" ,python2-pysam) - ("r-minimal" ,r-minimal) - ("r-deseq2" ,r-deseq2))) + (list coreutils + bedtools + python2-argparse + python2-pysam + r-minimal + r-deseq2)) (home-page "https://github.com/mhammell-laboratory/tetoolkit") (synopsis "Transposable elements in differential enrichment analysis") (description @@ -2615,7 +2549,7 @@ are not included due to their size.") (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) #t))))) (inputs - `(("perl" ,perl))) + (list perl)) (home-page "http://weizhongli-lab.org/cd-hit/") (synopsis "Cluster and compare protein or nucleotide sequences") (description @@ -2680,20 +2614,20 @@ setup")))) ;; This is not a library (delete 'sanity-check)))) (inputs - `(("htseq" ,htseq) - ("python-pybedtools" ,python-pybedtools) - ("python-cython" ,python-cython) - ("python-scikit-learn" ,python-scikit-learn) - ("python-matplotlib" ,python-matplotlib) - ("python-pandas" ,python-pandas) - ("python-pysam" ,python-pysam) - ("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy))) - (native-inputs - `(("python-setuptools-git" ,python-setuptools-git) - ("python-mock" ,python-mock) ; for tests - ("python-nose" ,python-nose) ; for tests - ("python-pytz" ,python-pytz))) ; for tests + (list htseq + python-pybedtools + python-cython + python-scikit-learn + python-matplotlib + python-pandas + python-pysam + python-numpy + python-scipy)) + (native-inputs + (list python-setuptools-git + python-mock ; for tests + python-nose ; for tests + python-pytz)) ; for tests (home-page "https://github.com/YeoLab/clipper") (synopsis "CLIP peak enrichment recognition") (description @@ -2729,7 +2663,7 @@ setup")))) (install-file "CodingQuarry" bin) (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)) #t))))) - (inputs `(("openmpi" ,openmpi))) + (inputs (list openmpi)) (native-search-paths (list (search-path-specification (variable "QUARRY_PATH") @@ -2754,7 +2688,7 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.") "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6")))) (build-system gnu-build-system) (inputs - `(("argtable" ,argtable))) + (list argtable)) (home-page "http://www.clustal.org/omega/") (synopsis "Multiple sequence aligner for protein and DNA/RNA") (description @@ -2782,14 +2716,10 @@ time.") (delete-file-recursively ".eggs"))))) (build-system python-build-system) (inputs - `(("python-bx-python" ,python-bx-python) - ("python-numpy" ,python-numpy) - ("python-pybigwig" ,python-pybigwig) - ("python-pysam" ,python-pysam) - ("zlib" ,zlib))) + (list python-bx-python python-numpy python-pybigwig python-pysam + zlib)) (native-inputs - `(("python-cython" ,python-cython) - ("python-nose" ,python-nose))) + (list python-cython python-nose)) (home-page "http://crossmap.sourceforge.net/") (synopsis "Convert genome coordinates between assemblies") (description @@ -2811,9 +2741,7 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") "14v5yyasq2bz34j38wi3xfcp06jj7l35ppibjcn95l2n73hz3zwi")))) (build-system python-build-system) (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ("python-xopen" ,python-xopen))) + (list python-cython python-pytest python-xopen)) (home-page "https://github.com/marcelm/dnaio/") (synopsis "Read FASTA and FASTQ files efficiently") (description @@ -2833,7 +2761,7 @@ files. The code was previously part of the cutadapt tool.") "1xnl80nblysj6dylj4683wgrfa425rkx4dp5k65hvwdns9pw753x")))) (build-system python-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/deeptools/deeptools_intervals") (synopsis "Create GTF-based interval trees with associated meta-data") (description @@ -2857,18 +2785,17 @@ interval trees with associated meta-data. It is primarily used by the "0l09vyynz6s6w7fnyd94rpys4a6aja6kp4gli64pngdxdz3md1nl")))) (build-system python-build-system) (native-inputs - `(("python-mock" ,python-mock) - ("python-nose" ,python-nose))) + (list python-mock python-nose)) (propagated-inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-numpydoc" ,python-numpydoc) - ("python-py2bit" ,python-py2bit) - ("python-pybigwig" ,python-pybigwig) - ("python-pysam" ,python-pysam) - ("python-scipy" ,python-scipy) - ("python-deeptoolsintervals" ,python-deeptoolsintervals) - ("python-plotly" ,python-plotly-2.4.1))) + (list python-matplotlib + python-numpy + python-numpydoc + python-py2bit + python-pybigwig + python-pysam + python-scipy + python-deeptoolsintervals + python-plotly-2.4.1)) (home-page "https://pypi.org/project/deepTools/") (synopsis "Useful tools for exploring deep sequencing data") (description "This package addresses the challenge of handling large amounts @@ -2907,12 +2834,9 @@ annotations of the genome.") (("os.path.exists\\('PKG-INFO'\\):") "os.path.exists('totally-does-not-exist'):"))))))) (inputs - `(("python-dnaio" ,python-dnaio) - ("python-xopen" ,python-xopen))) + (list python-dnaio python-xopen)) (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ("python-setuptools-scm" ,python-setuptools-scm))) + (list python-cython python-pytest python-setuptools-scm)) (home-page "https://cutadapt.readthedocs.io/en/stable/") (synopsis "Remove adapter sequences from nucleotide sequencing reads") (description @@ -2944,8 +2868,7 @@ other types of unwanted sequence from high-throughput sequencing reads.") (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("zlib" ,zlib) - ("curl" ,curl))) + (list zlib curl)) (native-inputs `(("doxygen" ,doxygen) ;; Need for tests @@ -2983,11 +2906,9 @@ files.") (("libs=\\[") "libs=[\"BigWig\", ")) #t))))) (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (inputs - `(("libbigwig" ,libbigwig) - ("zlib" ,zlib) - ("curl" ,curl))) + (list libbigwig zlib curl)) (home-page "https://github.com/dpryan79/pyBigWig") (synopsis "Access bigWig files in Python using libBigWig") (description @@ -3022,18 +2943,16 @@ accessing bigWig files.") "\"test requires network access\")\n" all)))))))) (propagated-inputs - `(("python-cachecontrol" ,python-cachecontrol) - ("python-lockfile" ,python-lockfile) - ("python-mistune" ,python-mistune) - ("python-rdflib" ,python-rdflib) - ("python-rdflib-jsonld" ,python-rdflib-jsonld) - ("python-requests" ,python-requests) - ("python-ruamel.yaml" ,python-ruamel.yaml) - ("python-typing-extensions" ,python-typing-extensions))) - (native-inputs - `(("python-black" ,python-black) - ("python-pytest" ,python-pytest) - ("python-pytest-runner" ,python-pytest-runner))) + (list python-cachecontrol + python-lockfile + python-mistune + python-rdflib + python-rdflib-jsonld + python-requests + python-ruamel.yaml + python-typing-extensions)) + (native-inputs + (list python-black python-pytest python-pytest-runner)) (home-page "https://github.com/common-workflow-language/schema_salad") (synopsis "Schema Annotations for Linked Avro Data (SALAD)") (description @@ -3105,30 +3024,30 @@ and record oriented data modeling and the Semantic Web.") (substitute* "tox.ini" (("-n auto") ""))))))) (propagated-inputs - `(("python-argcomplete" ,python-argcomplete) - ("python-bagit" ,python-bagit) - ("python-coloredlogs" ,python-coloredlogs) - ("python-mypy-extensions" ,python-mypy-extensions) - ("python-prov" ,python-prov) - ("python-pydot" ,python-pydot) - ("python-psutil" ,python-psutil) - ("python-rdflib" ,python-rdflib) - ("python-requests" ,python-requests) - ("python-ruamel.yaml" ,python-ruamel.yaml) - ("python-schema-salad" ,python-schema-salad) - ("python-shellescape" ,python-shellescape) - ("python-typing-extensions" ,python-typing-extensions) - ;; Not listed as needed but still necessary: - ("node" ,node))) - (native-inputs - `(("python-arcp" ,python-arcp) - ("python-humanfriendly" ,python-humanfriendly) - ("python-mock" ,python-mock) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-mock" ,python-pytest-mock) - ("python-pytest-runner" ,python-pytest-runner) - ("python-rdflib-jsonld" ,python-rdflib-jsonld))) + (list python-argcomplete + python-bagit + python-coloredlogs + python-mypy-extensions + python-prov + python-pydot + python-psutil + python-rdflib + python-requests + python-ruamel.yaml + python-schema-salad + python-shellescape + python-typing-extensions + ;; Not listed as needed but still necessary: + node)) + (native-inputs + (list python-arcp + python-humanfriendly + python-mock + python-pytest + python-pytest-cov + python-pytest-mock + python-pytest-runner + python-rdflib-jsonld)) (home-page "https://github.com/common-workflow-language/common-workflow-language") (synopsis "Common Workflow Language reference implementation") @@ -3257,10 +3176,7 @@ with Python.") (copy-recursively "excludeTemplates" templates) #t)))))) (inputs - `(("boost" ,boost) - ("bzip2" ,bzip2) - ("htslib" ,htslib) - ("zlib" ,zlib))) + (list boost bzip2 htslib zlib)) (home-page "https://github.com/dellytools/delly") (synopsis "Integrated structural variant prediction method") (description "Delly is an integrated structural variant prediction method @@ -3333,12 +3249,12 @@ bases are detected.") (wrap-program (string-append bin "/RepeatMasker") `("PERL5LIB" ":" prefix (,path ,share))))))))) (inputs - `(("perl" ,perl) - ("perl-text-soundex" ,perl-text-soundex) - ("python" ,python) - ("python-h5py" ,python-h5py) - ("hmmer" ,hmmer) - ("trf" ,trf))) + (list perl + perl-text-soundex + python + python-h5py + hmmer + trf)) (home-page "https://github.com/Benson-Genomics-Lab/TRF") (synopsis "Tandem Repeats Finder: a program to analyze DNA sequences") (description "A tandem repeat in DNA is two or more adjacent, approximate @@ -3373,7 +3289,7 @@ bases are detected.") (substitute* "CMakeLists.txt" (("-march=native") "")) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/bbuchfink/diamond") (synopsis "Accelerated BLAST compatible local sequence aligner") (description @@ -3428,9 +3344,7 @@ data and settings.") (("#define FASTA_HPP" line) (string-append line "\n#include <random>")))))))) (inputs - `(("boost" ,boost) - ("cairo" ,cairo) - ("rmath-standalone" ,rmath-standalone))) + (list boost cairo rmath-standalone)) (native-inputs `(("texlive" ,(texlive-updmap.cfg (list texlive-cm texlive-amsfonts @@ -3491,11 +3405,8 @@ of nucleic acid binding proteins.") (find-files "../bin" ".*")) #t)))))) (inputs - `(("gsl" ,gsl) - ("lapack" ,lapack) - ("openblas" ,openblas) - ("perl" ,perl) - ("gfortran" ,gfortran "lib"))) + (list gsl lapack openblas perl + `(,gfortran "lib"))) (home-page "https://github.com/DReichLab/EIG") (synopsis "Tools for population genetics") (description "The EIGENSOFT package provides tools for population @@ -3585,23 +3496,23 @@ quantitative phenotypes.") "-filter" "-help") #t))))) (inputs - `(("edirect-go-programs" ,edirect-go-programs) - ("perl-html-parser" ,perl-html-parser) - ("perl-encode-locale" ,perl-encode-locale) - ("perl-file-listing" ,perl-file-listing) - ("perl-html-tagset" ,perl-html-tagset) - ("perl-html-tree" ,perl-html-tree) - ("perl-http-cookies" ,perl-http-cookies) - ("perl-http-date" ,perl-http-date) - ("perl-http-message" ,perl-http-message) - ("perl-http-negotiate" ,perl-http-negotiate) - ("perl-lwp-mediatypes" ,perl-lwp-mediatypes) - ("perl-lwp-protocol-https" ,perl-lwp-protocol-https) - ("perl-net-http" ,perl-net-http) - ("perl-uri" ,perl-uri) - ("perl-www-robotrules" ,perl-www-robotrules) - ("perl-xml-simple" ,perl-xml-simple) - ("perl" ,perl))) + (list edirect-go-programs + perl-html-parser + perl-encode-locale + perl-file-listing + perl-html-tagset + perl-html-tree + perl-http-cookies + perl-http-date + perl-http-message + perl-http-negotiate + perl-lwp-mediatypes + perl-lwp-protocol-https + perl-net-http + perl-uri + perl-www-robotrules + perl-xml-simple + perl)) (home-page "https://www.ncbi.nlm.nih.gov/books/NBK179288/") (synopsis "Tools for accessing the NCBI's set of databases") (description @@ -3658,16 +3569,16 @@ software to answer ad hoc questions.") (native-inputs '()) (propagated-inputs '()) (inputs - `(("go-github-com-fatih-color" ,go-github-com-fatih-color) - ("go-github-com-fogleman-gg" ,go-github-com-fogleman-gg) - ("go-github-com-gedex-inflector" ,go-github-com-gedex-inflector) - ("go-github-com-golang-freetype" ,go-github-com-golang-freetype) - ("go-github-com-klauspost-cpuid" ,go-github-com-klauspost-cpuid) - ("go-github-com-pbnjay-memory" ,go-github-com-pbnjay-memory) - ("go-github-com-surgebase-porter2" ,go-github-com-surgebase-porter2) - ("go-golang-org-rainycape-unidecode" ,go-golang-org-rainycape-unidecode) - ("go-golang-org-x-image" ,go-golang-org-x-image) - ("go-golang-org-x-text" ,go-golang-org-x-text))))) + (list go-github-com-fatih-color + go-github-com-fogleman-gg + go-github-com-gedex-inflector + go-github-com-golang-freetype + go-github-com-klauspost-cpuid + go-github-com-pbnjay-memory + go-github-com-surgebase-porter2 + go-golang-org-rainycape-unidecode + go-golang-org-x-image + go-golang-org-x-text)))) (define-public exonerate (package @@ -3687,9 +3598,9 @@ software to answer ad hoc questions.") (arguments `(#:parallel-build? #f)) ; Building in parallel fails on some machines. (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("glib" ,glib))) + (list glib)) (home-page "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate") (synopsis "Generic tool for biological sequence alignment") @@ -3736,10 +3647,7 @@ dynamic programming or a variety of heuristics.") (("check_version\\(PACKAGE_VERSION\\);") "")) #t))))) (inputs - `(("boost" ,boost) - ("bamtools" ,bamtools) - ("protobuf" ,protobuf) - ("zlib" ,zlib))) + (list boost bamtools protobuf zlib)) (home-page "http://bio.math.berkeley.edu/eXpress") (synopsis "Streaming quantification for high-throughput genomic sequencing") (description @@ -3859,10 +3767,10 @@ reasonable amount of time and memory. For large alignments, FastTree is "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy")))) (build-system gnu-build-system) (inputs - `(("libgtextutils" ,libgtextutils))) + (list libgtextutils)) (native-inputs - `(("gcc" ,gcc-6) ;; doesn't build with later versions - ("pkg-config" ,pkg-config))) + (list gcc-6 ;; doesn't build with later versions + pkg-config)) (home-page "http://hannonlab.cshl.edu/fastx_toolkit/") (synopsis "Tools for FASTA/FASTQ file preprocessing") (description @@ -3909,11 +3817,9 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") (bin (string-append out "/bin/"))) (install-file "flexbar" bin))))))) (inputs - `(("tbb" ,tbb-2020) - ("zlib" ,zlib))) + (list tbb-2020 zlib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("seqan" ,seqan-2))) + (list pkg-config seqan-2)) (home-page "https://github.com/seqan/flexbar") (synopsis "Barcode and adapter removal tool for sequencing platforms") (description @@ -4052,8 +3958,7 @@ genes in incomplete assemblies or complete genomes.") (install-file "fxtract" bin) #t)))))) (inputs - `(("pcre" ,pcre) - ("zlib" ,zlib))) + (list pcre zlib)) (native-inputs ;; ctskennerton-util is licensed under GPL2. `(("ctskennerton-util" @@ -4100,9 +4005,7 @@ comment or quality sections.") #t)))) (build-system gnu-build-system) (inputs - `(("gsl" ,gsl) - ("openblas" ,openblas) - ("zlib" ,zlib))) + (list gsl openblas zlib)) (native-inputs `(("catch" ,catch-framework2-1) ("perl" ,perl) @@ -4166,12 +4069,9 @@ genome-wide association studies}.") (("Cython.Setup") "Cython.Build")) #t))))) (inputs - `(("python-scipy" ,python2-scipy) - ("python-numpy" ,python2-numpy) - ("python-pysam" ,python2-pysam) - ("python-networkx" ,python2-networkx))) + (list python2-scipy python2-numpy python2-pysam python2-networkx)) (native-inputs - `(("python-cython" ,python2-cython))) + (list python2-cython)) ;; The canonical <http://grit-bio.org> home page times out as of 2020-01-21. (home-page "https://github.com/nboley/grit") (synopsis "Tool for integrative analysis of RNA-seq type assays") @@ -4234,11 +4134,9 @@ estimates transcript expression.") "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))) (delete 'configure)))) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (inputs - `(("perl" ,perl) - ("python" ,python) - ("zlib" ,zlib))) + (list perl python zlib)) ;; Non-portable SSE instructions are used so building fails on platforms ;; other than x86_64. (supported-systems '("x86_64-linux")) @@ -4297,8 +4195,7 @@ particular, reads spanning multiple exons.") (mkdir-p doc) (install-file "doc/manual.inc.html" doc))))))) (native-inputs - `(("perl" ,perl) - ("pandoc" ,pandoc))) ; for documentation + (list perl pandoc)) ; for documentation (inputs `(("python" ,python-wrapper))) (home-page "https://daehwankimlab.github.io/hisat2/") @@ -4329,8 +4226,7 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") (base32 "0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj")))) (build-system gnu-build-system) - (native-inputs `(("perl" ,perl) - ("python" ,python))) ; for tests + (native-inputs (list perl python)) ; for tests (home-page "http://hmmer.org/") (synopsis "Biosequence analysis using profile hidden Markov models") (description @@ -4355,13 +4251,12 @@ HMMs).") "0pk41vkzxsbb5nv644325mh8akmz4zdply9r2s80dgg5b21pgp0b")))) (build-system python-build-system) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) ;; Numpy needs to be propagated when htseq is used as a Python library. (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (inputs - `(("python-pysam" ,python-pysam) - ("python-matplotlib" ,python-matplotlib))) + (list python-pysam python-matplotlib)) (home-page "https://htseq.readthedocs.io/") (synopsis "Analysing high-throughput sequencing data with Python") (description @@ -4411,7 +4306,7 @@ from high-throughput sequencing assays.") ("java-commons-jexl-2" ,java-commons-jexl-2) ("java-xz" ,java-xz))) (native-inputs - `(("java-testng" ,java-testng))) + (list java-testng)) (home-page "http://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description @@ -4454,7 +4349,7 @@ manipulating HTS data.") ("java-commons-jexl-2" ,java-commons-jexl-2) ("java-xz" ,java-xz))) (native-inputs - `(("java-junit" ,java-junit))) + (list java-junit)) (home-page "http://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description @@ -4557,10 +4452,9 @@ manipulating HTS data.") #t)) (replace 'install (install-jars "dist"))))) (inputs - `(("java-htsjdk" ,java-htsjdk) - ("java-guava" ,java-guava))) + (list java-htsjdk java-guava)) (native-inputs - `(("java-testng" ,java-testng))) + (list java-testng)) (home-page "http://broadinstitute.github.io/picard/") (synopsis "Tools for manipulating high-throughput sequencing data and formats") (description "Picard is a set of Java command line tools for manipulating @@ -4647,10 +4541,9 @@ Class-Path: /~a \ (rename-file "build.xml.new" "build.xml") #t))))) (propagated-inputs - `(("java-htsjdk" ,java-htsjdk-2.10.1))) + (list java-htsjdk-2.10.1)) (native-inputs - `(("java-testng" ,java-testng) - ("java-guava" ,java-guava))) + (list java-testng java-guava)) (home-page "http://broadinstitute.github.io/picard/") (synopsis "Tools for manipulating high-throughput sequencing data and formats") (description "Picard is a set of Java command line tools for manipulating @@ -4831,7 +4724,7 @@ VCF.") ("java-picard-1.113" ,java-picard-1.113) ("java-jbzip2" ,java-jbzip2))) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (home-page "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/") (synopsis "Quality control tool for high throughput sequence data") (description @@ -4880,7 +4773,7 @@ The main functions of FastQC are: (lambda* (#:key outputs #:allow-other-keys) (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/OpenGene/fastp/") (synopsis "All-in-one FastQ preprocessor") (description @@ -4910,13 +4803,12 @@ performance.") "--enable-libcurl" "--enable-s3"))) (inputs - `(("curl" ,curl) - ("openssl" ,openssl))) + (list curl openssl)) ;; This is referred to in the pkg-config file as a required library. (propagated-inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("perl" ,perl))) + (list perl)) (home-page "https://www.htslib.org") (synopsis "C library for reading/writing high-throughput sequencing data") (description @@ -5013,12 +4905,9 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and ;; causes the tests to always fail. (arguments `(#:tests? #f)) (propagated-inputs - `(("python-scipy" ,python-scipy) - ("python-sympy" ,python-sympy) - ("python-numpy" ,python-numpy) - ("python-matplotlib" ,python-matplotlib))) + (list python-scipy python-sympy python-numpy python-matplotlib)) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (home-page "https://github.com/nboley/idr") (synopsis "Tool to measure the irreproducible discovery rate (IDR)") (description @@ -5059,7 +4948,7 @@ experiments and provide highly stable thresholds based on reproducibility.") ("python" ,python-wrapper) ("pkg-config" ,pkg-config))) (inputs - `(("htslib" ,htslib))) + (list htslib)) (synopsis "Tool for fast counting of k-mers in DNA") (description "Jellyfish is a tool for fast, memory-efficient counting of k-mers in @@ -5140,15 +5029,9 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (add-installed-pythonpath inputs outputs) (invoke "pytest" "-v"))))))) (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest) - ("python-pytest-runner" ,python-pytest-runner))) + (list python-cython python-pytest python-pytest-runner)) (inputs - `(("zlib" ,zlib) - ("bzip2" ,bzip2) - ("seqan" ,seqan-1) - ("python-screed" ,python-screed) - ("python-bz2file" ,python-bz2file))) + (list zlib bzip2 seqan-1 python-screed python-bz2file)) (home-page "https://khmer.readthedocs.org/") (synopsis "K-mer counting, filtering and graph traversal library") (description "The khmer software is a set of command-line tools for @@ -5190,8 +5073,7 @@ data.") (copy-recursively "bin" bin)) #t))))) (inputs - `(("perl" ,perl) - ("zlib" ,zlib))) + (list perl zlib)) (home-page "http://kaiju.binf.ku.dk/") (synopsis "Fast and sensitive taxonomic classification for metagenomics") (description "Kaiju is a program for sensitive taxonomic classification @@ -5236,10 +5118,9 @@ experiments.") (add-installed-pythonpath inputs outputs) (invoke "pytest" "-v"))))))) (inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (native-inputs - `(("python-cython" ,python-cython) - ("python-pytest" ,python-pytest))) + (list python-cython python-pytest)) (home-page "https://github.com/macs3-project/MACS") (synopsis "Model based analysis for ChIP-Seq data") (description @@ -5319,11 +5200,7 @@ sequencing tag position and orientation.") `("PATH" ":" prefix (,path)))) (find-files bin)))))))) (inputs - `(("perl" ,perl) - ("ruby" ,ruby) - ("gawk" ,gawk) - ("grep" ,grep) - ("coreutils" ,coreutils))) + (list perl ruby gawk grep coreutils)) (home-page "https://mafft.cbrc.jp/alignment/software/") (synopsis "Multiple sequence alignment program") (description @@ -5380,14 +5257,14 @@ sequences).") (("c\\+\\+11") "c++14")) #t))))) (native-inputs - `(("autoconf" ,autoconf))) + (list autoconf)) (inputs - `(;; Capnproto and htslib are statically embedded in the final - ;; application. Therefore we also list their licenses, below. - ("capnproto" ,capnproto) - ("htslib" ,htslib) - ("gsl" ,gsl) - ("zlib" ,zlib))) + (list ;; Capnproto and htslib are statically embedded in the final + ;; application. Therefore we also list their licenses, below. + capnproto + htslib + gsl + zlib)) (supported-systems '("x86_64-linux")) (home-page "https://mash.readthedocs.io") (synopsis "Fast genome and metagenome distance estimation using MinHash") @@ -5439,11 +5316,7 @@ form of assemblies or reads.") (("set\\(Boost.*") "") (("add_dependencies.*") ""))))))) (inputs - `(("zlib" ,zlib) - ("perl" ,perl) - ("samtools" ,samtools) - ("htslib" ,htslib) - ("boost" ,boost))) + (list zlib perl samtools htslib boost)) (home-page "https://bitbucket.org/berkeleylab/metabat") (synopsis "Reconstruction of single genomes from complex microbial communities") @@ -5547,14 +5420,11 @@ linker_so='gcc -shared'); defines"))))) (inputs ;; Samtools must not be newer than 1.2. See ;; https://github.com/yarden/MISO/issues/135 - `(("samtools" ,samtools-1.2) - ("python-numpy" ,python2-numpy) - ("python-pysam" ,python2-pysam) - ("python-scipy" ,python2-scipy) - ("python-matplotlib" ,python2-matplotlib))) + (list samtools-1.2 python2-numpy python2-pysam python2-scipy + python2-matplotlib)) (native-inputs - `(("python-mock" ,python2-mock) ; for tests - ("python-pytz" ,python2-pytz))) ; for tests + (list python2-mock ; for tests + python2-pytz)) ; for tests (home-page "https://miso.readthedocs.io/en/fastmiso/") (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") (description @@ -5622,13 +5492,9 @@ program for nucleotide and protein sequences.") (inputs ;; XXX: TODO: Enable Lua and Guile bindings. ;; https://github.com/tjunier/newick_utils/issues/13 - `(("libxml2" ,libxml2) - ("flex" ,flex) - ("bison" ,bison))) + (list libxml2 flex bison)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) + (list autoconf automake libtool)) (synopsis "Programs for working with newick format phylogenetic trees") (description "Newick-utils is a suite of utilities for processing phylogenetic trees @@ -5650,11 +5516,9 @@ trimming, pruning, condensing, drawing (ASCII graphics or SVG).") (base32 "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr")))) (build-system gnu-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (native-inputs - `(("ruby-bio-commandeer" ,ruby-bio-commandeer) - ("ruby-rspec" ,ruby-rspec) - ("ruby" ,ruby))) + (list ruby-bio-commandeer ruby-rspec ruby)) (synopsis "Simple and not slow open reading frame (ORF) caller") (description "An ORF caller finds stretches of DNA that, when translated, are not @@ -5685,13 +5549,9 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") (("^sphinx") "")) #t))))) (propagated-inputs - `(("python-cython" ,python2-cython) - ("python-numpy" ,python2-numpy) - ("python-pysam" ,python2-pysam) - ("python-h5py" ,python2-h5py))) + (list python2-cython python2-numpy python2-pysam python2-h5py)) (native-inputs - `(("python-nose" ,python2-nose) - ("python-pyxb" ,python2-pyxb))) + (list python2-nose python2-pyxb)) (home-page "https://pacificbiosciences.github.io/pbcore/") (synopsis "Library for reading and writing PacBio data files") (description @@ -5723,17 +5583,15 @@ files and writing bioinformatics applications.") "from scipy import linalg\nimport weave")) #t))))) (propagated-inputs - `(("python-scipy" ,python2-scipy) - ("python-numpy" ,python2-numpy) - ("python-matplotlib" ,python2-matplotlib) - ("python-fastlmm" ,python2-fastlmm) - ("python-pandas" ,python2-pandas) - ("python-pysnptools" ,python2-pysnptools) - ("python-weave" ,python2-weave))) - (native-inputs - `(("python-mock" ,python2-mock) - ("python-nose" ,python2-nose) - ("unzip" ,unzip))) + (list python2-scipy + python2-numpy + python2-matplotlib + python2-fastlmm + python2-pandas + python2-pysnptools + python2-weave)) + (native-inputs + (list python2-mock python2-nose unzip)) (home-page "https://github.com/PMBio/warpedLMM") (synopsis "Implementation of warped linear mixed models") (description @@ -5781,9 +5639,7 @@ the phenotype as it models the data.") `("PATH" ":" prefix (,path))) (install-file "prank.1" man))))))) (inputs - `(("mafft" ,mafft) - ("exonerate" ,exonerate) - ("bppsuite" ,bppsuite))) + (list mafft exonerate bppsuite)) (home-page "http://wasabiapp.org/software/prank/") (synopsis "Probabilistic multiple sequence alignment program") (description @@ -5855,7 +5711,7 @@ predicts the locations of structural units in the sequences.") ("lapack" ,lapack) ("openblas" ,openblas))) (native-inputs - `(("which" ,which))) + (list which)) (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") (synopsis "Detect orthologous genes across species") (description @@ -5884,7 +5740,7 @@ large-scale data and can be applied to hundreds of species at once.") `(#:python ,python-2 ; does not work with Python 3 #:tests? #f)) ; there are no tests (inputs - `(("python2-matplotlib" ,python2-matplotlib))) + (list python2-matplotlib)) (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo") (synopsis "Analyze high-throughput genetic sequencing data") (description @@ -6008,10 +5864,7 @@ partial genes, and identifies translation initiation sites.") (,(string-append coreutils-path ":" out "/bin")))))) #t))))) (native-inputs - `(("perl-env-path" ,perl-env-path) - ("perl-test-files" ,perl-test-files) - ("perl-test-most" ,perl-test-most) - ("perl-test-output" ,perl-test-output))) + (list perl-env-path perl-test-files perl-test-most perl-test-output)) (inputs `(("perl-array-utils" ,perl-array-utils) ("bioperl" ,bioperl-minimal) @@ -6084,7 +5937,7 @@ extremely diverse sets of genomes.") (symlink (string-append bin "/" executable) "raxml")) #t))))) (inputs - `(("openmpi" ,openmpi))) + (list openmpi)) (home-page "https://cme.h-its.org/exelixis/web/software/raxml/index.html") (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees") (description @@ -6172,11 +6025,7 @@ phylogenies.") "rsem-run-ebseq" "rsem-run-prsem-testing-procedure")))))))) (inputs - `(("boost" ,boost) - ("r-minimal" ,r-minimal) - ("perl" ,perl) - ("htslib" ,htslib-1.3) - ("zlib" ,zlib))) + (list boost r-minimal perl htslib-1.3 zlib)) (home-page "http://deweylab.biostat.wisc.edu/rsem/") (synopsis "Estimate gene expression levels from RNA-Seq data") (description @@ -6204,14 +6053,14 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") "0gbb9iyb7swiv5455fm5rg98r7l6qn27v564yllqjd574hncpx6m")))) (build-system python-build-system) (inputs - `(("python-cython" ,python-cython) - ("python-bx-python" ,python-bx-python) - ("python-pybigwig" ,python-pybigwig) - ("python-pysam" ,python-pysam) - ("python-numpy" ,python-numpy) - ("zlib" ,zlib))) + (list python-cython + python-bx-python + python-pybigwig + python-pysam + python-numpy + zlib)) (native-inputs - `(("python-nose" ,python-nose))) + (list python-nose)) (home-page "http://rseqc.sourceforge.net/") (synopsis "RNA-seq quality control package") (description @@ -6271,7 +6120,7 @@ distribution, coverage uniformity, strand specificity, etc.") ("python" ,python) ("readline" ,readline))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://seek.princeton.edu") (synopsis "Gene co-expression search engine") (description @@ -6329,13 +6178,9 @@ to the user's query of interest.") (install-file file include)) (scandir "." (lambda (name) (string-match "\\.h$" name)))) #t)))))) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs (list pkg-config)) (inputs - `(("htslib" ,htslib) - ("ncurses" ,ncurses) - ("perl" ,perl) - ("python" ,python) - ("zlib" ,zlib))) + (list htslib ncurses perl python zlib)) (home-page "http://samtools.sourceforge.net") (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") (description @@ -6364,11 +6209,7 @@ viewer.") (delete-file-recursively "htslib-1.10") #t)))) (inputs - `(("htslib" ,htslib-1.10) - ("ncurses" ,ncurses) - ("perl" ,perl) - ("python" ,python) - ("zlib" ,zlib))))) + (list htslib-1.10 ncurses perl python zlib)))) (define-public samtools-1.2 (package (inherit samtools) @@ -6423,15 +6264,9 @@ viewer.") (("P 52.out.*") "")))) (delete 'configure)))) (native-inputs - `(("grep" ,grep) - ("gawk" ,gawk) - ("pkg-config" ,pkg-config))) + (list grep gawk pkg-config)) (inputs - `(("htslib" ,htslib-for-samtools-1.2) - ("ncurses" ,ncurses) - ("perl" ,perl) - ("python" ,python) - ("zlib" ,zlib))))) + (list htslib-for-samtools-1.2 ncurses perl python zlib)))) (define-public samtools-0.1 ;; This is the most recent version of the 0.1 line of samtools. The input @@ -6543,8 +6378,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (mkdir-p share) (copy-recursively "../R" share))))))) (inputs - `(("boost" ,boost) - ("htslib" ,htslib))) + (list boost htslib)) (home-page "https://github.com/friendsofstrandseq/mosaicatcher") (synopsis "Count and classify Strand-seq reads") (description @@ -6586,7 +6420,7 @@ each chromosome in each cell using a Hidden Markov Model.") #t))) (add-after 'unpack 'enter-dir (lambda _ (chdir "ngs-sdk") #t))))) - (native-inputs `(("perl" ,perl))) + (native-inputs (list perl)) ;; According to the test ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) ;; in ngs-sdk/setup/konfigure.perl @@ -6724,7 +6558,7 @@ simultaneously.") ("java-ngs" ,java-ngs) ("libmagic" ,file) ("hdf5" ,hdf5))) - (native-inputs `(("perl" ,perl))) + (native-inputs (list perl)) ;; NCBI-VDB requires SSE capability. (supported-systems '("i686-linux" "x86_64-linux")) (home-page "https://github.com/ncbi/ncbi-vdb") @@ -6770,10 +6604,9 @@ accessed/downloaded on demand across HTTP.") "/bin/"))) (install-file "plink" bin))))))) (inputs - `(("zlib" ,zlib) - ("lapack" ,lapack))) + (list zlib lapack)) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/") (synopsis "Whole genome association analysis toolset") (description @@ -6830,13 +6663,9 @@ subsequent visualization, annotation and storage of results.") (invoke "bash" "test_setup.sh") (invoke "python3" "tests.py")))))))) (inputs - `(("lapack" ,lapack) - ("openblas" ,openblas) - ("zlib" ,zlib))) + (list lapack openblas zlib)) (native-inputs - `(("diffutils" ,diffutils) - ("plink" ,plink) - ("python" ,python))) ; for tests + (list diffutils plink python)) ; for tests (home-page "https://www.cog-genomics.org/plink/") (license license:gpl3+))) @@ -6883,8 +6712,7 @@ subsequent visualization, annotation and storage of results.") #t)) (delete 'configure)))) (inputs - `(("samtools" ,samtools-0.1) - ("zlib" ,zlib))) + (list samtools-0.1 zlib)) (home-page "https://github.com/smithlabcode/smithlab_cpp") (synopsis "C++ helper library for functions used in Smith lab projects") (description @@ -6924,10 +6752,7 @@ structures, classes for genomic regions, mapped sequencing reads, etc.") "PROGS=preseq" "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)"))) (inputs - `(("gsl" ,gsl) - ("samtools" ,samtools-0.1) - ("smithlab-cpp" ,smithlab-cpp) - ("zlib" ,zlib))) + (list gsl samtools-0.1 smithlab-cpp zlib)) (home-page "http://smithlabresearch.org/software/preseq/") (synopsis "Program for analyzing library complexity") (description @@ -6953,11 +6778,9 @@ complexity samples.") "148vcb7w2wr6a4w6vs2bsxanbqibxfk490zbcbg4m61s8669zdjx")))) (build-system python-build-system) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-runner" ,python-pytest-runner))) + (list python-pytest python-pytest-cov python-pytest-runner)) (inputs - `(("python-bz2file" ,python-bz2file))) + (list python-bz2file)) (home-page "https://github.com/dib-lab/screed/") (synopsis "Short read sequence database utilities") (description "Screed parses FASTA and FASTQ files and generates databases. @@ -7055,7 +6878,7 @@ sequence itself can be retrieved from these databases.") (string-append "--with-hdf5-prefix=" (assoc-ref inputs "hdf5"))) #t))))) - (native-inputs `(("perl" ,perl))) + (native-inputs (list perl)) (inputs `(("ngs-sdk" ,ngs-sdk) ("ncbi-vdb" ,ncbi-vdb) @@ -7093,9 +6916,7 @@ writing files into the .sra format.") (lambda _ (invoke "ctest" "test" "--output-on-failure")))))) (native-inputs - `(("bzip2" ,bzip2) - ("cereal" ,cereal) - ("zlib" ,zlib))) + (list bzip2 cereal zlib)) (home-page "https://www.seqan.de") (synopsis "Library for nucleotide sequence analysis") (description @@ -7188,9 +7009,9 @@ bioinformatics file formats, sequence alignment, and more.") "0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b")))) (build-system python-build-system) (inputs - `(("python-biopython" ,python-biopython))) + (list python-biopython)) (native-inputs - `(("python-nose" ,python-nose))) + (list python-nose)) (home-page "https://github.com/fhcrc/seqmagick") (synopsis "Tools for converting and modifying sequence files") (description @@ -7228,7 +7049,7 @@ is one that takes arguments.") (install-file "seqtk" bin) #t)))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/lh3/seqtk") (synopsis "Toolkit for processing biological sequences in FASTA/Q format") (description @@ -7265,7 +7086,7 @@ optionally compressed by gzip.") (install-file "snap-aligner" bin) (install-file "SNAPCommand" bin))))))) (native-inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "http://snap.cs.berkeley.edu/") (synopsis "Short read DNA sequence aligner") (description @@ -7313,7 +7134,7 @@ of these reads to align data quickly through a hash-based indexing scheme.") (find-files "rRNA_databases" ".*fasta")) #t)))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://bioinfo.lifl.fr/RNA/sortmerna/") (synopsis "Biological sequence analysis tool for NGS reads") (description @@ -7395,10 +7216,9 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") #t)) (delete 'configure)))) (native-inputs - `(("xxd" ,xxd))) + (list xxd)) (inputs - `(("htslib" ,htslib) - ("zlib" ,zlib))) + (list htslib zlib)) (home-page "https://github.com/alexdobin/STAR") (synopsis "Universal RNA-seq aligner") (description @@ -7505,7 +7325,7 @@ sequences.") (copy-recursively "../bin" bin)))) ;; no "configure" script (delete 'configure)))) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (home-page "http://subread.sourceforge.net/") (synopsis "Tool kit for processing next-gen sequencing data") (description @@ -7562,8 +7382,7 @@ against local background noises.") (install-file "stringtie" bin) #t)))))) (inputs - `(("samtools" ,samtools-0.1) - ("zlib" ,zlib))) + (list samtools-0.1 zlib)) (home-page "http://ccb.jhu.edu/software/stringtie/") (synopsis "Transcript assembly and quantification for RNA-Seq data") (description @@ -7617,16 +7436,16 @@ Cuffdiff or Ballgown programs.") ;; available. (delete 'sanity-check)))) (propagated-inputs - `(("python-sqlalchemy" ,python-sqlalchemy) - ("python-decorator" ,python-decorator) - ("python-biopython" ,python-biopython) - ("python-pandas" ,python-pandas) - ("python-psycopg2" ,python-psycopg2) - ("python-fastalite" ,python-fastalite) - ("python-pyyaml" ,python-pyyaml) - ("python-six" ,python-six) - ("python-jinja2" ,python-jinja2) - ("python-dendropy" ,python-dendropy))) + (list python-sqlalchemy + python-decorator + python-biopython + python-pandas + python-psycopg2 + python-fastalite + python-pyyaml + python-six + python-jinja2 + python-dendropy)) (home-page "https://github.com/fhcrc/taxtastic") (synopsis "Tools for taxonomic naming and annotation") (description @@ -7656,10 +7475,9 @@ profiles, and associated taxonomic information.") (string-append "PREFIX=" #$output) (string-append "MANDIR=" #$output "/share/man/man1")))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("perl" ,perl) - ("zlib" ,zlib))) + (list perl zlib)) (home-page "https://vcftools.github.io/") (synopsis "Tools for working with VCF files") (description @@ -7684,8 +7502,7 @@ data in the form of VCF files.") "1z4mgwqg1j4n5ika08ai8mg9yjyjhf4821jp83v2bgwzxrykqjgr")))) (build-system gnu-build-system) (native-inputs - `(("perl" ,perl) - ("python" ,python))) ; for tests + (list perl python)) ; for tests (home-page "http://eddylab.org/infernal/") (synopsis "Inference of RNA alignments") (description "Infernal (\"INFERence of RNA ALignment\") is a tool for @@ -7718,15 +7535,15 @@ sequence.") (properties `((upstream . "presto"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr))) + (list r-data-table + r-deseq2 + r-dplyr + r-matrix + r-rcpp + r-rcpparmadillo + r-reshape2 + r-rlang + r-tidyr)) (home-page "https://github.com/immunogenomics/presto") (synopsis "Fast Functions for Differential Expression using Wilcox and AUC") (description "This package performs a fast Wilcoxon rank sum test and @@ -7749,25 +7566,25 @@ auROC analysis.") (properties `((upstream-name . "SnapATAC"))) (build-system r-build-system) (propagated-inputs - `(("r-bigmemory" ,r-bigmemory) - ("r-doparallel" ,r-doparallel) - ("r-dosnow" ,r-dosnow) - ("r-edger" ,r-edger) - ("r-foreach" ,r-foreach) - ("r-genomicranges" ,r-genomicranges) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-plot3d" ,r-plot3d) - ("r-rann" ,r-rann) - ("r-raster" ,r-raster) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rhdf5" ,r-rhdf5) - ("r-rtsne" ,r-rtsne) - ("r-scales" ,r-scales) - ("r-viridis" ,r-viridis))) + (list r-bigmemory + r-doparallel + r-dosnow + r-edger + r-foreach + r-genomicranges + r-igraph + r-iranges + r-irlba + r-matrix + r-plyr + r-plot3d + r-rann + r-raster + r-rcolorbrewer + r-rhdf5 + r-rtsne + r-scales + r-viridis)) (home-page "https://github.com/r3fang/SnapATAC") (synopsis "Single nucleus analysis package for ATAC-Seq") (description @@ -7812,12 +7629,10 @@ single cell ATAC-seq sequencing data.") (("\"perl") (string-append "\"" (which "perl"))))))))) (inputs - `(("perl" ,perl) - ("bowtie" ,bowtie))) + (list perl bowtie)) (propagated-inputs - `(("r-misha" ,r-misha) - ("r-zoo" ,r-zoo))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-misha r-zoo)) + (native-inputs (list r-knitr)) (home-page "https://github.com/tanaylab/umi4cpackage") (synopsis "Processing and analysis of UMI-4C contact profiles") (description "This is a package that lets you process UMI-4C data from @@ -7844,16 +7659,16 @@ scratch to produce nice plots.") (properties `((upstream-name . "ShinyCell"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-gridextra" ,r-gridextra) - ("r-hdf5r" ,r-hdf5r) - ("r-matrix" ,r-matrix) - ("r-r-utils" ,r-r-utils) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-readr" ,r-readr) - ("r-reticulate" ,r-reticulate))) + (list r-data-table + r-ggplot2 + r-glue + r-gridextra + r-hdf5r + r-matrix + r-r-utils + r-rcolorbrewer + r-readr + r-reticulate)) (home-page "https://github.com/SGDDNB/ShinyCell") (synopsis "Shiny interactive web apps for single-cell data") (description @@ -7880,30 +7695,30 @@ single-cell data.") (properties `((upstream-name . "ArchR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-chromvar" ,r-chromvar) - ("r-complexheatmap" ,r-complexheatmap) - ("r-data-table" ,r-data-table) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-gtools" ,r-gtools) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-motifmatchr" ,r-motifmatchr) - ("r-nabor" ,r-nabor) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5" ,r-rhdf5) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-uwot" ,r-uwot))) + (list r-biocgenerics + r-biostrings + r-chromvar + r-complexheatmap + r-data-table + r-genomicranges + r-ggplot2 + r-ggrepel + r-gridextra + r-gtable + r-gtools + r-magrittr + r-matrix + r-matrixstats + r-motifmatchr + r-nabor + r-plyr + r-rcpp + r-rhdf5 + r-rsamtools + r-s4vectors + r-stringr + r-summarizedexperiment + r-uwot)) (home-page "https://github.com/GreenleafLab/ArchR") (synopsis "Analyze single-cell regulatory chromatin in R") (description @@ -7925,21 +7740,21 @@ single-cell data.") "10na2gyka24mszdxf92wz9h2c13hdf1ww30c68gfsw53lvvhhhxb")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-mgcv" ,r-mgcv) - ("r-rook" ,r-rook) - ("r-rjson" ,r-rjson) - ("r-cairo" ,r-cairo) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-edger" ,r-edger) - ("r-quantreg" ,r-quantreg) - ("r-nnet" ,r-nnet) - ("r-rmtstat" ,r-rmtstat) - ("r-extremes" ,r-extremes) - ("r-pcamethods" ,r-pcamethods) - ("r-biocparallel" ,r-biocparallel) - ("r-flexmix" ,r-flexmix))) + (list r-rcpp + r-rcpparmadillo + r-mgcv + r-rook + r-rjson + r-cairo + r-rcolorbrewer + r-edger + r-quantreg + r-nnet + r-rmtstat + r-extremes + r-pcamethods + r-biocparallel + r-flexmix)) (home-page "https://hms-dbmi.github.io/scde/") (synopsis "R package for analyzing single-cell RNA-seq data") (description "The SCDE package implements a set of statistical methods for @@ -7981,7 +7796,7 @@ of transcriptional heterogeneity among single cells.") (assoc-ref inputs "kentutils") "/bin/bigWigToWig")))))))) (inputs - `(("kentutils" ,kentutils))) + (list kentutils)) (home-page "https://github.com/tanaylab/misha") (synopsis "Toolkit for analysis of genomic data") (description "This package is intended to help users to efficiently @@ -8009,18 +7824,18 @@ analyze genomic data resulting from various experiments.") '(delete-file "inst/doc/shaman-package.R")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-domc" ,r-domc) - ("r-ggplot2" ,r-ggplot2) - ("r-gviz" ,r-gviz) - ("r-misha" ,r-misha) - ("r-plyr" ,r-plyr) - ("r-rann" ,r-rann) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ;; For vignettes - ("r-rmarkdown" ,r-rmarkdown) - ("r-knitr" ,r-knitr))) + (list r-data-table + r-domc + r-ggplot2 + r-gviz + r-misha + r-plyr + r-rann + r-rcpp + r-reshape2 + ;; For vignettes + r-rmarkdown + r-knitr)) (home-page "https://github.com/tanaylab/shaman") (synopsis "Sampling HiC contact matrices for a-parametric normalization") (description "The Shaman package implements functions for @@ -8075,11 +7890,7 @@ information as possible.") (properties `((upstream-name . "deMULTIplex"))) (build-system r-build-system) (propagated-inputs - `(("r-kernsmooth" ,r-kernsmooth) - ("r-reshape2" ,r-reshape2) - ("r-rtsne" ,r-rtsne) - ("r-shortread" ,r-shortread) - ("r-stringdist" ,r-stringdist))) + (list r-kernsmooth r-reshape2 r-rtsne r-shortread r-stringdist)) (home-page "https://github.com/chris-mcginnis-ucsf/MULTI-seq") (synopsis "MULTI-seq pre-processing and classification tools") (description @@ -8118,17 +7929,17 @@ includes software to (substitute* "requirements.txt" (("==") ">="))))))) (inputs - `(("python-cryptography" ,python-cryptography) - ("python-intervaltree" ,python-intervaltree) - ("python-jsonschema" ,python-jsonschema) - ("python-lxml" ,python-lxml) - ("python-ndg-httpsclient" ,python-ndg-httpsclient) - ("python-progressbar2" ,python-progressbar2) - ("python-pyasn1" ,python-pyasn1) - ("python-pyopenssl" ,python-pyopenssl) - ("python-pyyaml" ,python-pyyaml) - ("python-requests" ,python-requests) - ("python-termcolor" ,python-termcolor))) + (list python-cryptography + python-intervaltree + python-jsonschema + python-lxml + python-ndg-httpsclient + python-progressbar2 + python-pyasn1 + python-pyopenssl + python-pyyaml + python-requests + python-termcolor)) (home-page "https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool") (synopsis "GDC data transfer tool") (description "The gdc-client provides several convenience functions over @@ -8160,12 +7971,9 @@ the GDC API which provides general download/upload via HTTPS.") #t)))) (build-system gnu-build-system) (inputs - `(("zlib" ,zlib) - ("bzip2" ,bzip2) - ("cityhash" ,cityhash))) + (list zlib bzip2 cityhash)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake))) + (list autoconf automake)) (synopsis "Sequence search tools for metagenomics") (description "VSEARCH supports DNA sequence searching, clustering, chimera detection, @@ -8204,8 +8012,7 @@ Needleman-Wunsch).") (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "ParDRe" bin))))))) (inputs - `(("openmpi-c++" ,openmpi-c++) - ("zlib" ,zlib))) + (list openmpi-c++ zlib)) (synopsis "Parallel tool to remove duplicate DNA reads") (description "ParDRe is a parallel tool to remove duplicate genetic sequence reads. @@ -8236,7 +8043,7 @@ clusters.") (build-system cmake-build-system) (arguments '(#:tests? #false)) ; there are none (inputs - `(("boost" ,boost))) + (list boost)) (home-page "https://github.com/cbg-ethz/ngshmmalign/") (synopsis "Profile HMM aligner for NGS reads") (description @@ -8282,14 +8089,14 @@ experience substantial biological insertions and deletions.") (,(getenv "PERL5LIB"))))) scripts))))))) (inputs - `(("guile" ,guile-3.0) ; for wrapper scripts - ("perl" ,perl) - ("perl-cairo" ,perl-cairo) - ("perl-data-dumper" ,perl-data-dumper) - ("perl-digest-md5" ,perl-digest-md5) - ("perl-getopt-long" ,perl-getopt-long) - ("perl-json" ,perl-json) - ("perl-statistics-pca" ,perl-statistics-pca))) + (list guile-3.0 ; for wrapper scripts + perl + perl-cairo + perl-data-dumper + perl-digest-md5 + perl-getopt-long + perl-json + perl-statistics-pca)) (home-page "http://prinseq.sourceforge.net/") (synopsis "Preprocess sequence data in FASTA or FASTQ formats") (description @@ -8340,14 +8147,14 @@ data. It also generates basic statistics for your sequences.") (when tests? (invoke "make" "check"))))))) (inputs - `(("boost" ,boost) - ("htslib" ,htslib) - ("python" ,python) - ("python-biopython" ,python-biopython) - ("python-numpy" ,python-numpy) - ("zlib" ,zlib))) + (list boost + htslib + python + python-biopython + python-numpy + zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "") (synopsis "Short reads assembly into haplotypes") (description @@ -8372,11 +8179,9 @@ frequency of the different genetic variants present in a mixed sample.") (arguments `(#:test-target "spec")) (native-inputs - `(("bundler" ,bundler) - ("ruby-rspec" ,ruby-rspec) - ("ruby-rake-compiler" ,ruby-rake-compiler))) + (list bundler ruby-rspec ruby-rake-compiler)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (synopsis "Ruby bindings for the kseq.h FASTA/Q parser") (description "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and @@ -8398,7 +8203,7 @@ quality scores.") "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0")))) (build-system ruby-build-system) (native-inputs - `(("ruby-rspec" ,ruby-rspec))) + (list ruby-rspec)) (synopsis "Tool for fast querying of genome locations") (description "Bio-locus is a tabix-like tool for fast querying of genome @@ -8421,10 +8226,9 @@ chr+pos+alt information in a database.") "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692")))) (build-system ruby-build-system) (propagated-inputs - `(("ruby-bio-logger" ,ruby-bio-logger) - ("ruby-nokogiri" ,ruby-nokogiri))) + (list ruby-bio-logger ruby-nokogiri)) (inputs - `(("ruby-rspec" ,ruby-rspec))) + (list ruby-rspec)) (synopsis "Fast big data BLAST XML parser and library") (description "Very fast parallel big-data BLAST XML file parser which can be used as @@ -8446,9 +8250,9 @@ generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.") "1d56amdsjv1mag7m6gv2w0xij8hqx1v5xbdjsix8sp3yp36m7938")))) (build-system ruby-build-system) (propagated-inputs - `(("ruby-libxml" ,ruby-libxml))) + (list ruby-libxml)) (native-inputs - `(("which" ,which))) ; required for test phase + (list which)) ; required for test phase (arguments `(#:phases (modify-phases %standard-phases @@ -8489,7 +8293,7 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") "1glw5pn9s8z13spxk6yyfqaz80n9lga67f33w35nkpq9dwi2vg6g")))) (build-system ruby-build-system) (native-inputs - `(("ruby-cucumber" ,ruby-cucumber))) + (list ruby-cucumber)) (synopsis "Smart VCF parser DSL") (description "Bio-vcf provides a @acronym{DSL, domain specific language} for processing @@ -8532,16 +8336,16 @@ including VCF header and contents in RDF and JSON.") (inputs `(("r" ,r-minimal))) (propagated-inputs - `(("r-catools" ,r-catools) - ("r-snow" ,r-snow) - ("r-snowfall" ,r-snowfall) - ("r-bitops" ,r-bitops) - ("r-rsamtools" ,r-rsamtools) - ("r-spp" ,r-spp) - ("gawk" ,gawk) - ("samtools" ,samtools) - ("boost" ,boost) - ("gzip" ,gzip))) + (list r-catools + r-snow + r-snowfall + r-bitops + r-rsamtools + r-spp + gawk + samtools + boost + gzip)) (home-page "https://github.com/kundajelab/phantompeakqualtools") (synopsis "Informative enrichment for ChIP-seq data") (description "This package computes informative enrichment and quality @@ -8564,8 +8368,7 @@ characteristic tag shift values in these assays.") "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5")))) (build-system r-build-system) (propagated-inputs - `(("r-optparse" ,r-optparse) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-optparse r-rcolorbrewer)) (home-page "https://www.e-rna.org/r-chie/index.cgi") (synopsis "Analysis framework for RNA secondary structure") (description @@ -8617,7 +8420,7 @@ secondary structure and comparative analysis in R.") ("guile-json" ,guile-json-1) ("guile-redis" ,guile2.2-redis))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/BIMSBbioinfo/rcas-web") (synopsis "Web interface for RNA-centric annotation system (RCAS)") (description "This package provides a simple web interface for the @@ -8642,16 +8445,16 @@ secondary structure and comparative analysis in R.") "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0")))) (build-system r-build-system) (propagated-inputs - `(("r-iranges" ,r-iranges) - ("r-xvector" ,r-xvector) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-gtools" ,r-gtools) - ("r-genomicranges" ,r-genomicranges) - ("r-sfsmisc" ,r-sfsmisc) - ("r-kernlab" ,r-kernlab) - ("r-s4vectors" ,r-s4vectors) - ("r-biocgenerics" ,r-biocgenerics))) + (list r-iranges + r-xvector + r-biostrings + r-bsgenome + r-gtools + r-genomicranges + r-sfsmisc + r-kernlab + r-s4vectors + r-biocgenerics)) (home-page "https://github.com/ManuSetty/ChIPKernels") (synopsis "Build string kernels for DNA Sequence analysis") (description "ChIPKernels is an R package for building different string @@ -8676,12 +8479,12 @@ Sequences.") "1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799")))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-chipkernels" ,r-chipkernels) - ("r-genomicranges" ,r-genomicranges) - ("r-spams" ,r-spams) - ("r-wgcna" ,r-wgcna) - ("r-fastcluster" ,r-fastcluster))) + (list r-biostrings + r-chipkernels + r-genomicranges + r-spams + r-wgcna + r-fastcluster)) (home-page "https://github.com/ManuSetty/SeqGL") (synopsis "Group lasso for Dnase/ChIP-seq data") (description "SeqGL is a group lasso based algorithm to extract @@ -8731,17 +8534,14 @@ AM_CONDITIONAL(AMPNG, true)")) (add-after 'disable-update-check 'autogen (lambda _ (invoke "autoreconf" "-vif") #t))))) (inputs - `(("perl" ,perl) - ("libpng" ,libpng) - ("gd" ,gd) - ("libx11" ,libx11) - ("libharu" ,libharu) - ("zlib" ,zlib))) + (list perl + libpng + gd + libx11 + libharu + zlib)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool) - ("pkg-config" ,pkg-config))) + (list autoconf automake libtool pkg-config)) (home-page "http://emboss.sourceforge.net") (synopsis "Molecular biology analysis suite") (description "EMBOSS is the \"European Molecular Biology Open Software @@ -8789,8 +8589,7 @@ tools for sequence analysis into a seamless whole.") "bin" (string-append (assoc-ref outputs "out") "/bin")) #t))))) (inputs - `(("gsl" ,gsl) - ("zlib" ,zlib))) + (list gsl zlib)) (home-page "https://github.com/arq5x/bits") (synopsis "Implementation of binary interval search algorithm") (description "This package provides an implementation of the @@ -8880,9 +8679,7 @@ may optionally be provided to further inform the peak-calling process.") `(#:python ,python-2 ; python2 only #:tests? #f)) ; no tests included (propagated-inputs - `(("python2-numpy" ,python2-numpy) - ("python2-scipy" ,python2-scipy) - ("python2-pysam" ,python2-pysam))) + (list python2-numpy python2-scipy python2-pysam)) (home-page "https://github.com/shawnzhangyx/PePr") (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data") (description @@ -8957,20 +8754,20 @@ replacement for strverscmp.") ;; reasons. (delete 'sanity-check)))) (propagated-inputs - `(("python-click" ,python-click) - ("python-coloredlogs" ,python-coloredlogs) - ("python-future" ,python-future) - ("python-jinja2" ,python-jinja2) - ("python-lzstring" ,python-lzstring) - ("python-markdown" ,python-markdown) - ("python-matplotlib" ,python-matplotlib) - ("python-networkx" ,python-networkx) - ("python-numpy" ,python-numpy) - ("python-pyyaml" ,python-pyyaml) - ("python-requests" ,python-requests) - ("python-rich" ,python-rich) - ("python-simplejson" ,python-simplejson) - ("python-spectra" ,python-spectra))) + (list python-click + python-coloredlogs + python-future + python-jinja2 + python-lzstring + python-markdown + python-matplotlib + python-networkx + python-numpy + python-pyyaml + python-requests + python-rich + python-simplejson + python-spectra)) (native-inputs `(("python-pytest" ,python-pytest) ("tests" @@ -9009,19 +8806,16 @@ common bioinformatics tools.") "12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g")))) (build-system python-build-system) (inputs - `(("boost" ,boost) - ("c-blosc" ,c-blosc) - ("gsl" ,gsl) - ("hdf5" ,hdf5) - ("hdf5-blosc" ,hdf5-blosc) - ("python-cython" ,python-cython) - ("zlib" ,zlib))) + (list boost + c-blosc + gsl + hdf5 + hdf5-blosc + python-cython + zlib)) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-pycurl" ,python-pycurl) - ("python-pyzmq" ,python-pyzmq) - ("python-scipy" ,python-scipy) - ("python-tables" ,python-tables))) + (list python-numpy python-pycurl python-pyzmq python-scipy + python-tables)) (home-page "https://vatlab.github.io/vat-docs/") (synopsis "Analyze genetic variants from Next-Gen sequencing studies") (description @@ -9047,11 +8841,7 @@ manipulate and analyze genetic variants.") (properties `((upstream-name . "RareMETALS2"))) (build-system r-build-system) (propagated-inputs - `(("r-seqminer" ,r-seqminer) - ("r-mvtnorm" ,r-mvtnorm) - ("r-mass" ,r-mass) - ("r-compquadform" ,r-compquadform) - ("r-getopt" ,r-getopt))) + (list r-seqminer r-mvtnorm r-mass r-compquadform r-getopt)) (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2") (synopsis "Analyze gene-level association tests for binary trait") (description @@ -9082,11 +8872,7 @@ trait.") "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-gridextra" ,r-gridextra) - ("r-gplots" ,r-gplots) - ("r-plyr" ,r-plyr))) + (list r-ggplot2 r-rcolorbrewer r-gridextra r-gplots r-plyr)) (home-page "https://github.com/rajewsky-lab/dropbead") (synopsis "Basic exploration and analysis of Drop-seq data") (description "This package offers a quick and straight-forward way to @@ -9118,41 +8904,41 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (properties `((upstream-name . "CellChat"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-circlize" ,r-circlize) - ("r-colorspace" ,r-colorspace) - ("r-complexheatmap" ,r-complexheatmap) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-expm" ,r-expm) - ("r-fnn" ,r-fnn) - ("r-forcats" ,r-forcats) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-gg-gap" ,r-gg-gap) - ("r-ggalluvial" ,r-ggalluvial) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-nmf" ,r-nmf) - ("r-patchwork" ,r-patchwork) - ("r-pbapply" ,r-pbapply) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-reshape2" ,r-reshape2) - ("r-reticulate" ,r-reticulate) - ("r-rspectra" ,r-rspectra) - ("r-rtsne" ,r-rtsne) - ("r-scales" ,r-scales) - ("r-shape" ,r-shape) - ("r-sna" ,r-sna) - ("r-stringr" ,r-stringr) - ("r-svglite" ,r-svglite))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-circlize + r-colorspace + r-complexheatmap + r-cowplot + r-dplyr + r-expm + r-fnn + r-forcats + r-future + r-future-apply + r-gg-gap + r-ggalluvial + r-ggplot2 + r-ggrepel + r-igraph + r-irlba + r-magrittr + r-matrix + r-nmf + r-patchwork + r-pbapply + r-rcolorbrewer + r-rcpp + r-rcppeigen + r-reshape2 + r-reticulate + r-rspectra + r-rtsne + r-scales + r-shape + r-sna + r-stringr + r-svglite)) + (native-inputs (list r-knitr)) (home-page "https://github.com/sqjin/CellChat") (synopsis "Analysis of cell-cell communication from single-cell transcriptomics data") (description @@ -9198,11 +8984,9 @@ communication networks from scRNA-seq data.") (copy-file (string-append "bin/sambamba-" ,version) (string-append bin "/sambamba")))))))) (native-inputs - `(("python" ,python))) + (list python)) (inputs - `(("ldc" ,ldc) - ("lz4" ,lz4) - ("zlib" ,zlib))) + (list ldc lz4 zlib)) (home-page "https://github.com/biod/sambamba") (synopsis "Tools for working with SAM/BAM data") (description "Sambamba is a high performance modern robust and @@ -9245,10 +9029,7 @@ sort, markdup, and depth.") (install-file "bin/Ritornello" bin) #t)))))) (inputs - `(("samtools" ,samtools-0.1) - ("fftw" ,fftw) - ("boost" ,boost) - ("zlib" ,zlib))) + (list samtools-0.1 fftw boost zlib)) (home-page "https://github.com/KlugerLab/Ritornello") (synopsis "Control-free peak caller for ChIP-seq data") (description "Ritornello is a ChIP-seq peak calling algorithm based on @@ -9314,12 +9095,9 @@ with narrow binding events such as transcription factor ChIP-seq.") (install-file "trim_galore" bin) #t)))))) (inputs - `(("gzip" ,gzip) - ("perl" ,perl) - ("pigz" ,pigz) - ("cutadapt" ,cutadapt))) + (list gzip perl pigz cutadapt)) (native-inputs - `(("unzip" ,unzip))) + (list unzip)) (home-page "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/") (synopsis "Wrapper around Cutadapt and FastQC") (description "Trim Galore! is a wrapper script to automate quality and @@ -9465,22 +9243,19 @@ programs for inferring phylogenies (evolutionary trees).") `(("python" ,python-wrapper) ("swig" ,swig))) (inputs - `(("boost" ,boost) - ("cgal" ,cgal) - ("gsl" ,gsl) - ("hdf5" ,hdf5) - ("fftw" ,fftw) - ("eigen" ,eigen) - ;; Enabling MPI causes the build to use all the available memory and - ;; fail (tested on a machine with 32 GiB of RAM). - ;;("mpi" ,openmpi) - ("opencv" ,opencv))) + (list boost + cgal + gsl + hdf5 + fftw + eigen + ;; Enabling MPI causes the build to use all the available memory and + ;; fail (tested on a machine with 32 GiB of RAM). + ;;("mpi" ,openmpi) + opencv)) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-pandas" ,python-pandas) - ("python-scikit-learn" ,python-scikit-learn) - ("python-networkx" ,python-networkx))) + (list python-numpy python-scipy python-pandas python-scikit-learn + python-networkx)) (home-page "https://integrativemodeling.org") (synopsis "Integrative modeling platform") (description "IMP's broad goal is to contribute to a comprehensive @@ -9538,18 +9313,18 @@ applications for tackling some common problems in a user-friendly way.") (add-installed-pythonpath inputs outputs) (invoke "python3" "test/test_all.py"))))))) (native-inputs - `(("glib" ,glib "bin") ;for gtester - ("pkg-config" ,pkg-config))) + (list `(,glib "bin") ;for gtester + pkg-config)) (inputs ;; TODO: add Chimera for visualization - `(("imp" ,imp) - ("mcl" ,mcl) - ("python-future" ,python-future) - ("python-h5py" ,python-h5py) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-matplotlib" ,python-matplotlib) - ("python-pysam" ,python-pysam))) + (list imp + mcl + python-future + python-h5py + python-scipy + python-numpy + python-matplotlib + python-pysam)) (home-page "https://3dgenomes.github.io/TADbit/") (synopsis "Analyze, model, and explore 3C-based data") (description @@ -9728,8 +9503,7 @@ browser.") (install-file "build~/fseq.jar" lib) (copy-recursively "lib" lib))))))) (inputs - `(("perl" ,perl) - ("java-commons-cli" ,java-commons-cli))) + (list perl java-commons-cli)) (home-page "https://fureylab.web.unc.edu/software/fseq/") (synopsis "Feature density estimator for high-throughput sequence tags") (description @@ -9815,9 +9589,7 @@ Browser.") "/bin/gunzip -c"))) #t)))))) (inputs - `(("gzip" ,gzip) - ("perl-carp" ,perl-carp) - ("perl-getopt-long" ,perl-getopt-long))) + (list gzip perl-carp perl-getopt-long)) (native-inputs `(("plotly.js" ,(origin @@ -9926,11 +9698,9 @@ using nucleotide or amino-acid sequence data.") (install-file exe bin)) exes))))))) (inputs - `(("htslib" ,htslib) - ("ncurses" ,ncurses) - ("zlib" ,zlib))) + (list htslib ncurses zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://www.bioinf.uni-leipzig.de/Software/segemehl") (synopsis "Map short sequencer reads to reference genomes") (description "Segemehl is software to map short sequencer reads to @@ -9979,9 +9749,7 @@ output of segemehl is a SAM or BAM formatted alignment file.") (("include_directories\\(\\.\\./ext/htslib\\)") "")) #t))))) (inputs - `(("hdf5" ,hdf5) - ("htslib" ,htslib-1.9) - ("zlib" ,zlib))) + (list hdf5 htslib-1.9 zlib)) (home-page "https://pachterlab.github.io/kallisto/") (synopsis "Near-optimal RNA-Seq quantification") (description @@ -10147,7 +9915,7 @@ dependency like SeqAn.") ("tbb" ,tbb-2020) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://www.cs.cmu.edu/~ckingsf/software/sailfish/") (synopsis "Mapping-based isoform quantification from RNA-Seq reads") (description "Sailfish is a tool for genomic transcript quantification @@ -10322,7 +10090,7 @@ The following file formats are supported: ("xz" ,xz) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/COMBINE-lab/salmon") (synopsis "Quantification from RNA-seq reads using lightweight alignments") (description "Salmon is a program to produce highly-accurate, @@ -10355,12 +10123,9 @@ variational inference.") (lambda _ (invoke "pytest" "tests")))))) (propagated-inputs - `(("python-h5py" ,python-h5py) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-scipy" ,python-scipy))) + (list python-h5py python-numpy python-pandas python-scipy)) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/linnarsson-lab/loompy") (synopsis "Work with .loom files for single-cell RNA-seq data") (description "The loom file format is an efficient format for very large @@ -10382,7 +10147,7 @@ single-cell RNA-seq data.") (base32 "0bccs37d5saxn5xsd2rfpkrnc5a120xs3ibizai66fgvp1vxbnc4")))) (build-system python-build-system) (arguments `(#:tests? #false)) ; require internet access - (propagated-inputs `(("python-requests" ,python-requests))) + (propagated-inputs (list python-requests)) (home-page "https://github.com/biothings/biothings_client.py") (synopsis "Python client for BioThings API services") (description "This package provides a Python client for BioThings @@ -10401,7 +10166,7 @@ API services.") (base32 "1snszwdgfygchxshcbry3b5pbcw3g1isp8dw46razxccqaxwlag7")))) (build-system python-build-system) (propagated-inputs - `(("python-biothings-client" ,python-biothings-client))) + (list python-biothings-client)) (home-page "https://github.com/biothings/mygene.py") (synopsis "Python Client for MyGene.Info services.") (description "MyGene.Info provides simple-to-use REST web services @@ -10477,8 +10242,7 @@ MyGene.Info services.") ;; There is no install target (replace 'install (install-jars "."))))) (propagated-inputs - `(("java-commons-codec" ,java-commons-codec) - ("java-openchart2" ,java-openchart2))) + (list java-commons-codec java-openchart2)) (home-page "https://sites.google.com/site/cmzmasek/home/software/forester") (synopsis "Phylogenomics libraries for Java") (description "Forester is a collection of Java libraries for @@ -10550,8 +10314,7 @@ reading, writing, and exporting phylogenetic trees.") ;; There is no install target (replace 'install (install-jars "."))))) (propagated-inputs - `(("java-commons-codec" ,java-commons-codec) - ("java-openchart2" ,java-openchart2))) + (list java-commons-codec java-openchart2)) ;; The source archive does not contain the resources. (native-inputs `(("phyloxml.xsd" @@ -10619,13 +10382,10 @@ reading, writing, and exporting phylogenetic trees.") "build/test-classes") #t))))) (propagated-inputs - `(("java-log4j-api" ,java-log4j-api) - ("java-log4j-core" ,java-log4j-core) - ("java-slf4j-api" ,java-slf4j-api) - ("java-slf4j-simple" ,java-slf4j-simple))) + (list java-log4j-api java-log4j-core java-slf4j-api + java-slf4j-simple)) (native-inputs - `(("java-junit" ,java-junit) - ("java-hamcrest-core" ,java-hamcrest-core))) + (list java-junit java-hamcrest-core)) (home-page "https://biojava.org") (synopsis "Core libraries of Java framework for processing biological data") (description "BioJava is a project dedicated to providing a Java framework @@ -10660,15 +10420,14 @@ This package provides the core libraries.") "build/test-classes") #t))))) (propagated-inputs - `(("java-log4j-api" ,java-log4j-api) - ("java-log4j-core" ,java-log4j-core) - ("java-slf4j-api" ,java-slf4j-api) - ("java-slf4j-simple" ,java-slf4j-simple) - ("java-biojava-core" ,java-biojava-core) - ("java-forester" ,java-forester))) - (native-inputs - `(("java-junit" ,java-junit) - ("java-hamcrest-core" ,java-hamcrest-core))) + (list java-log4j-api + java-log4j-core + java-slf4j-api + java-slf4j-simple + java-biojava-core + java-forester)) + (native-inputs + (list java-junit java-hamcrest-core)) (home-page "https://biojava.org") (synopsis "Biojava interface to the forester phylogenomics library") (description "The phylo module provides a biojava interface layer to the @@ -10696,16 +10455,15 @@ forester phylogenomics library for constructing phylogenetic trees."))) "build/test-classes") #t))))) (propagated-inputs - `(("java-log4j-api" ,java-log4j-api) - ("java-log4j-core" ,java-log4j-core) - ("java-slf4j-api" ,java-slf4j-api) - ("java-slf4j-simple" ,java-slf4j-simple) - ("java-biojava-core" ,java-biojava-core) - ("java-biojava-phylo" ,java-biojava-phylo) - ("java-forester" ,java-forester))) - (native-inputs - `(("java-junit" ,java-junit) - ("java-hamcrest-core" ,java-hamcrest-core))) + (list java-log4j-api + java-log4j-core + java-slf4j-api + java-slf4j-simple + java-biojava-core + java-biojava-phylo + java-forester)) + (native-inputs + (list java-junit java-hamcrest-core)) (home-page "https://biojava.org") (synopsis "Biojava API for genetic sequence alignment") (description "The alignment module of BioJava provides an API that @@ -10754,15 +10512,14 @@ contains "build/test-classes") #t))))) (propagated-inputs - `(("java-log4j-api" ,java-log4j-api) - ("java-log4j-core" ,java-log4j-core) - ("java-slf4j-api" ,java-slf4j-api) - ("java-slf4j-simple" ,java-slf4j-simple) - ("java-biojava-core" ,java-biojava-core-4.0) - ("java-forester" ,java-forester-1.005))) - (native-inputs - `(("java-junit" ,java-junit) - ("java-hamcrest-core" ,java-hamcrest-core))) + (list java-log4j-api + java-log4j-core + java-slf4j-api + java-slf4j-simple + java-biojava-core-4.0 + java-forester-1.005)) + (native-inputs + (list java-junit java-hamcrest-core)) (home-page "https://biojava.org") (synopsis "Biojava interface to the forester phylogenomics library") (description "The phylo module provides a biojava interface layer to the @@ -10790,16 +10547,15 @@ forester phylogenomics library for constructing phylogenetic trees."))) "build/test-classes") #t))))) (propagated-inputs - `(("java-log4j-api" ,java-log4j-api) - ("java-log4j-core" ,java-log4j-core) - ("java-slf4j-api" ,java-slf4j-api) - ("java-slf4j-simple" ,java-slf4j-simple) - ("java-biojava-core" ,java-biojava-core-4.0) - ("java-biojava-phylo" ,java-biojava-phylo-4.0) - ("java-forester" ,java-forester-1.005))) - (native-inputs - `(("java-junit" ,java-junit) - ("java-hamcrest-core" ,java-hamcrest-core))) + (list java-log4j-api + java-log4j-core + java-slf4j-api + java-slf4j-simple + java-biojava-core-4.0 + java-biojava-phylo-4.0 + java-forester-1.005)) + (native-inputs + (list java-junit java-hamcrest-core)) (home-page "https://biojava.org") (synopsis "Biojava API for genetic sequence alignment") (description "The alignment module of BioJava provides an API that @@ -10940,8 +10696,7 @@ contains ("java-simple-xml" ,java-simple-xml) ("java-snakeyaml" ,java-snakeyaml))) (native-inputs - `(("unzip" ,unzip) - ("java-testng" ,java-testng))) + (list unzip java-testng)) (home-page "http://mccarrolllab.com/dropseq/") (synopsis "Tools for Drop-seq analyses") (description "Drop-seq is a technology to enable biologists to @@ -10985,44 +10740,42 @@ once. This package provides tools to perform Drop-seq analyses.") (search-input-directory inputs "share/zoneinfo"))))))) (inputs - `(("coreutils" ,coreutils) - ("sed" ,sed) - ("gzip" ,gzip) - ("snakemake" ,snakemake) - ("multiqc" ,multiqc) - ("star" ,star-for-pigx) - ("hisat2" ,hisat2) - ("fastp" ,fastp) - ("htseq" ,htseq) - ("samtools" ,samtools) - ("r-minimal" ,r-minimal) - ("r-rmarkdown" ,r-rmarkdown) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-ggrepel" ,r-ggrepel) - ("r-gprofiler2" ,r-gprofiler2) - ("r-deseq2" ,r-deseq2) - ("r-dt" ,r-dt) - ("r-knitr" ,r-knitr) - ("r-pheatmap" ,r-pheatmap) - ("r-corrplot" ,r-corrplot) - ("r-reshape2" ,r-reshape2) - ("r-plotly" ,r-plotly) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-crosstalk" ,r-crosstalk) - ("r-tximport" ,r-tximport) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rjson" ,r-rjson) - ("salmon" ,salmon) - ("pandoc" ,pandoc) - ("python-wrapper" ,python-wrapper) - ("python-deeptools" ,python-deeptools) - ("python-pyyaml" ,python-pyyaml))) - (native-inputs - `(("tzdata" ,tzdata) - ("automake" ,automake) - ("autoconf" ,autoconf))) + (list coreutils + sed + gzip + snakemake + multiqc + star-for-pigx + hisat2 + fastp + htseq + samtools + r-minimal + r-rmarkdown + r-ggplot2 + r-ggpubr + r-ggrepel + r-gprofiler2 + r-deseq2 + r-dt + r-knitr + r-pheatmap + r-corrplot + r-reshape2 + r-plotly + r-scales + r-summarizedexperiment + r-crosstalk + r-tximport + r-rtracklayer + r-rjson + salmon + pandoc + python-wrapper + python-deeptools + python-pyyaml)) + (native-inputs + (list tzdata automake autoconf)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for RNA sequencing experiments") (description "PiGX RNAseq is an analysis pipeline for preprocessing and @@ -11055,58 +10808,56 @@ expression report comparing samples in an easily configurable manner.") (lambda _ (invoke "autoreconf" "-vif")))))) (inputs - `(("grep" ,grep) - ("coreutils" ,coreutils) - ("r-minimal" ,r-minimal) - ("r-argparser" ,r-argparser) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-chipseq" ,r-chipseq) - ("r-corrplot" ,r-corrplot) - ("r-data-table" ,r-data-table) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gprofiler2" ,r-gprofiler2) - ("r-heatmaply" ,r-heatmaply) - ("r-hexbin" ,r-hexbin) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rsamtools" ,r-rsamtools) - ("r-rsubread" ,r-rsubread) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("python-wrapper" ,python-wrapper) - ("python-pyyaml" ,python-pyyaml) - ("python-magic" ,python-magic) - ("python-xlrd" ,python-xlrd) - ("trim-galore" ,trim-galore) - ("macs" ,macs) - ("multiqc" ,multiqc) - ("perl" ,perl) - ("pandoc" ,pandoc) - ("fastqc" ,fastqc) - ("bowtie" ,bowtie) - ("idr" ,idr) - ("snakemake" ,snakemake) - ("samtools" ,samtools) - ("bedtools" ,bedtools) - ("kentutils" ,kentutils))) - (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("python-pytest" ,python-pytest))) + (list grep + coreutils + r-minimal + r-argparser + r-biocparallel + r-biostrings + r-chipseq + r-corrplot + r-data-table + r-deseq2 + r-dplyr + r-dt + r-genomation + r-genomicalignments + r-genomicranges + r-ggplot2 + r-ggrepel + r-gprofiler2 + r-heatmaply + r-hexbin + r-htmlwidgets + r-jsonlite + r-pheatmap + r-plotly + r-rmarkdown + r-rsamtools + r-rsubread + r-rtracklayer + r-s4vectors + r-stringr + r-tibble + r-tidyr + python-wrapper + python-pyyaml + python-magic + python-xlrd + trim-galore + macs + multiqc + perl + pandoc + fastqc + bowtie + idr + snakemake + samtools + bedtools + kentutils)) + (native-inputs + (list autoconf automake python-pytest)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for ChIP sequencing experiments") (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak @@ -11149,41 +10900,39 @@ in an easily configurable manner.") (search-input-directory inputs "share/zoneinfo"))))))) (native-inputs - `(("tzdata" ,tzdata) - ("automake" ,automake) - ("autoconf" ,autoconf))) - (inputs - `(("coreutils" ,coreutils) - ("sed" ,sed) - ("grep" ,grep) - ("r-minimal" ,r-minimal) - ("r-annotationhub" ,r-annotationhub) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-ggbio" ,r-ggbio) - ("r-ggrepel" ,r-ggrepel) - ("r-matrixstats" ,r-matrixstats) - ("r-methylkit" ,r-methylkit) - ("r-reshape2" ,r-reshape2) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-bookdown" ,r-bookdown) - ("r-ggplot2" ,r-ggplot2) - ("r-ggbio" ,r-ggbio) - ("pandoc" ,pandoc) - ("python-wrapper" ,python-wrapper) - ("python-pyyaml" ,python-pyyaml) - ("snakemake" ,snakemake) - ("bismark" ,bismark) - ("bowtie" ,bowtie) - ("bwa-meth" ,bwa-meth) - ("fastqc" ,fastqc) - ("methyldackel" ,methyldackel) - ("multiqc" ,multiqc) - ("trim-galore" ,trim-galore) - ("cutadapt" ,cutadapt) - ("samblaster" ,samblaster) - ("samtools" ,samtools))) + (list tzdata automake autoconf)) + (inputs + (list coreutils + sed + grep + r-minimal + r-annotationhub + r-dt + r-genomation + r-ggbio + r-ggrepel + r-matrixstats + r-methylkit + r-reshape2 + r-rtracklayer + r-rmarkdown + r-bookdown + r-ggplot2 + r-ggbio + pandoc + python-wrapper + python-pyyaml + snakemake + bismark + bowtie + bwa-meth + fastqc + methyldackel + multiqc + trim-galore + cutadapt + samblaster + samtools)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports") (description "PiGx BSseq is a data processing pipeline for raw fastq read @@ -11213,8 +10962,7 @@ methylation and segmentation.") (lambda _ (invoke "autoreconf" "-vif")))))) (native-inputs - `(("automake" ,automake) - ("autoconf" ,autoconf))) + (list automake autoconf)) (inputs `(("coreutils" ,coreutils) ("perl" ,perl) @@ -11288,40 +11036,39 @@ based methods.") (lambda _ (invoke "autoreconf" "-vif")))))) (native-inputs - `(("automake" ,automake) - ("autoconf" ,autoconf))) - (inputs - `(("bash-minimal" ,bash-minimal) - ("bbmap" ,bbmap) - ("bedtools" ,bedtools) - ("bwa" ,bwa) - ("ensembl-vep" ,ensembl-vep) - ("fastp" ,fastp) - ("fastqc" ,fastqc) - ("ivar" ,ivar) - ("kraken2" ,kraken2) - ("krona-tools" ,krona-tools) - ("lofreq" ,lofreq) - ("multiqc" ,multiqc) - ("prinseq" ,prinseq) - ("python-pyyaml" ,python-pyyaml) - ("python-wrapper" ,python-wrapper) - ("r-base64url" ,r-base64url) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-minimal" ,r-minimal) - ("r-plotly" ,r-plotly) - ("r-qpcr" ,r-qpcr) - ("r-r-utils" ,r-r-utils) - ("r-reshape2" ,r-reshape2) - ("r-rmarkdown" ,r-rmarkdown) - ("r-stringr" ,r-stringr) - ("r-tidyr" ,r-tidyr) - ("samtools" ,samtools) - ("snakemake" ,snakemake) - ("wget" ,wget))) + (list automake autoconf)) + (inputs + (list bash-minimal + bbmap + bedtools + bwa + ensembl-vep + fastp + fastqc + ivar + kraken2 + krona-tools + lofreq + multiqc + prinseq + python-pyyaml + python-wrapper + r-base64url + r-dplyr + r-dt + r-ggplot2 + r-magrittr + r-minimal + r-plotly + r-qpcr + r-r-utils + r-reshape2 + r-rmarkdown + r-stringr + r-tidyr + samtools + snakemake + wget)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for wastewater sequencing") (description "PiGx SARS-CoV-2 is a pipeline for analysing data from @@ -11345,11 +11092,7 @@ variant abundance over time and location.") "1i5njdy1clj5ncw45d16p7mwmqvb1ilikl9n797pxklc3f4s7mq7")))) (build-system gnu-build-system) (inputs - `(("python" ,python) - ("pigx-bsseq" ,pigx-bsseq) - ("pigx-chipseq" ,pigx-chipseq) - ("pigx-rnaseq" ,pigx-rnaseq) - ("pigx-scrnaseq" ,pigx-scrnaseq))) + (list python pigx-bsseq pigx-chipseq pigx-rnaseq pigx-scrnaseq)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipelines for genomics") (description "PiGx is a collection of genomics pipelines. It includes the @@ -11391,7 +11134,7 @@ HTML reports with interesting findings about your samples.") (install-file "Genrich" (string-append (assoc-ref outputs "out") "/bin")) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/jsh58/Genrich") (synopsis "Detecting sites of genomic enrichment") (description "Genrich is a peak-caller for genomic enrichment @@ -11421,11 +11164,9 @@ enrichment.") '(#:tests? #f ; there are none #:configure-flags (list "-DNH=ON"))) ; do not use SSE4.2 instructions (inputs - `(("sdsl-lite" ,sdsl-lite) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list sdsl-lite openssl zlib)) (native-inputs - `(("gcc" ,gcc-7))) + (list gcc-7)) (home-page "https://github.com/splatlab/mantis") (synopsis "Large-scale sequence-search index data structure") (description "Mantis is a space-efficient data structure that can be @@ -11480,8 +11221,7 @@ analyses in addition to large-scale sequence-level searches.") "/bin"))) '("j_count" "b_count" "sjcount"))))))) (inputs - `(("samtools" ,samtools-0.1) - ("zlib" ,zlib))) + (list samtools-0.1 zlib)) (home-page "https://github.com/pervouchine/sjcount-full/") (synopsis "Annotation-agnostic splice junction counting pipeline") (description "Sjcount is a utility for fast quantification of splice @@ -11556,7 +11296,7 @@ version does count multisplits.") out ,version)))) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://lh3.github.io/minimap2/") (synopsis "Pairwise aligner for genomic and spliced nucleotide sequences") (description "Minimap2 is a versatile sequence alignment program that @@ -11587,9 +11327,9 @@ cases include: "1a05p7rkmxa6qhm108na8flzj2v45jab06drk59kzk1ip2sgvzqq")))) (build-system python-build-system) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/lh3/minimap2") (synopsis "Python binding for minimap2") (description "This package provides a convenient interface to minimap2, @@ -11612,7 +11352,7 @@ sequences.") "04dv5wv8bhsw1imxwyd438bnn9kby7svp44nbcz8lsadzjjci5gs")))) (build-system gnu-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (arguments `(#:tests? #f ; There are no tests. #:phases @@ -11670,10 +11410,9 @@ Thus the per-base error rate is similar to the raw input reads.") (install-file "Bandage" (string-append out "/bin")) #t)))))) (inputs - `(("qtbase" ,qtbase-5) - ("qtsvg" ,qtsvg))) + (list qtbase-5 qtsvg)) (native-inputs - `(("imagemagick" ,imagemagick))) + (list imagemagick)) (home-page "https://rrwick.github.io/Bandage/") (synopsis "Bioinformatics Application for Navigating De novo Assembly Graphs Easily") @@ -11709,10 +11448,10 @@ contigs alone.") ;; The test suite attempts to execute ../test-driver, which does not exist. (arguments '(#:tests? #false)) (propagated-inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("gcc" ,gcc-10) ;Code has C++17 requirements - ("pkg-config" ,pkg-config))) + (list gcc-10 ;Code has C++17 requirements + pkg-config)) (home-page "https://gitlab.com/german.tischler/libmaus2") (synopsis "Collection of data structures and algorithms useful for bioinformatics") (description "libmaus2 is a collection of data structures and @@ -11753,11 +11492,10 @@ and many lower level support classes. ,#~(list (string-append "--with-libmaus2=" #$(this-package-input "libmaus2"))))) (inputs - `(("libmaus2" ,libmaus2) - ("xerces-c" ,xerces-c))) + (list libmaus2 xerces-c)) (native-inputs - `(("gcc" ,gcc-10) ;Code has C++17 requirements - ("pkg-config" ,pkg-config))) + (list gcc-10 ;Code has C++17 requirements + pkg-config)) (home-page "https://gitlab.com/german.tischler/biobambam2") (synopsis "Tools for processing BAM files") (description "This package contains some tools for processing BAM files @@ -11798,23 +11536,23 @@ including: "0jhjn3ilb057hbf6yzrihj13ifxxs32y7nkby8l3lkm28dg4p97h")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biomart" ,r-biomart) - ("r-data-table" ,r-data-table) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hash" ,r-hash) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rmysql" ,r-rmysql) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationhub + r-biomart + r-data-table + r-dbi + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-hash + r-iranges + r-rcolorbrewer + r-rmysql + r-s4vectors + r-stringr + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/BIMSBbioinfo/ciRcus") (synopsis "Annotation, analysis and visualization of circRNA data") (description "Circus is an R package for annotation, analysis and @@ -11927,9 +11665,7 @@ conversions, region filtering, FASTA sequence extraction and more.") "unmapped2anchors.py"))) #t))))) (inputs - `(("python2" ,python-2) - ("python2-pysam" ,python2-pysam) - ("python2-numpy" ,python2-numpy))) + (list python-2 python2-pysam python2-numpy)) (home-page "https://github.com/marvin-jens/find_circ") (synopsis "circRNA detection from RNA-seq reads") (description "This package provides tools to detect head-to-tail @@ -11980,7 +11716,7 @@ in RNA-seq data.") (string-append "FAST_TSNE_SCRIPT_DIR = \"" out "\"\n"))) (install-file "fast_tsne.R" share))))))) (inputs - `(("fftw" ,fftw))) + (list fftw)) (home-page "https://github.com/KlugerLab/FIt-SNE") (synopsis "Fast Fourier Transform-accelerated interpolation-based t-SNE") (description "@dfn{t-Stochastic Neighborhood Embedding} (t-SNE) is a @@ -12078,28 +11814,28 @@ implementation differs in these ways: " and not test_pca_sparse" " and not test_pca_reproducible")))))))) (propagated-inputs - `(("python-anndata" ,python-anndata) - ("python-h5py" ,python-h5py) - ("python-igraph" ,python-igraph) - ("python-joblib" ,python-joblib) - ("python-legacy-api-wrap" ,python-legacy-api-wrap) - ("python-louvain" ,python-louvain-0.6) - ("python-matplotlib" ,python-matplotlib) - ("python-natsort" ,python-natsort) - ("python-networkx" ,python-networkx) - ("python-numba" ,python-numba) - ("python-packaging" ,python-packaging) - ("python-pandas" ,python-pandas) - ("python-patsy" ,python-patsy) - ("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy) - ("python-seaborn" ,python-seaborn) - ("python-sinfo" ,python-sinfo) - ("python-statsmodels" ,python-statsmodels) - ("python-tables" ,python-tables) - ("python-pytoml" ,python-pytoml) - ("python-tqdm" ,python-tqdm) - ("python-umap-learn" ,python-umap-learn))) + (list python-anndata + python-h5py + python-igraph + python-joblib + python-legacy-api-wrap + python-louvain-0.6 + python-matplotlib + python-natsort + python-networkx + python-numba + python-packaging + python-pandas + python-patsy + python-scikit-learn + python-scipy + python-seaborn + python-sinfo + python-statsmodels + python-tables + python-pytoml + python-tqdm + python-umap-learn)) (native-inputs `(;; This package needs anndata.tests, which is not installed. ("python-anndata:source" ,(package-source python-anndata)) @@ -12138,12 +11874,12 @@ million cells.") (substitute* "setup.py" (("'sklearn'") ""))))))) (propagated-inputs - `(("python-annoy" ,python-annoy) - ("python-cython" ,python-cython) - ("python-numpy" ,python-numpy) - ("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy) - ("python-umap-learn" ,python-umap-learn))) + (list python-annoy + python-cython + python-numpy + python-scikit-learn + python-scipy + python-umap-learn)) (home-page "https://github.com/Teichlab/bbknn") (synopsis "Batch balanced KNN") (description "BBKNN is a batch effect removal tool that can be directly @@ -12171,14 +11907,14 @@ altering the counts or PCA space.") "08vk0x6v5c5n7afgd5pcjhsvb424absypxy22hw1cm1n9kirbi77")))) (build-system python-build-system) (propagated-inputs - `(("python-biopython" ,python-biopython) - ("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pytest" ,python-pytest) - ("python-scikit-learn" ,python-scikit-learn) - ("python-seaborn" ,python-seaborn) - ("python-tqdm" ,python-tqdm))) + (list python-biopython + python-matplotlib + python-numpy + python-pandas + python-pytest + python-scikit-learn + python-seaborn + python-tqdm)) (home-page "https://github.com/MrOlm/drep") (synopsis "De-replication of microbial genomes assembled from multiple samples") (description @@ -12211,24 +11947,24 @@ set.") (("from job_utils") "from .job_utils"))))))) (inputs - `(("python-biopython" ,python-biopython-1.73) - ("python-boto3" ,python-boto3) - ("python-h5py" ,python-h5py) - ("python-lmfit" ,python-lmfit) - ("python-matplotlib" ,python-matplotlib) - ("python-networkx" ,python-networkx) - ("python-numba" ,python-numba) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-psutil" ,python-psutil) - ("python-pysam" ,python-pysam) - ("python-scikit-learn" ,python-scikit-learn) - ("python-seaborn" ,python-seaborn) - ("python-tqdm" ,python-tqdm) - ;; drep is needed for deprecated plot utilities - ("python-drep" ,python-drep))) - (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-biopython-1.73 + python-boto3 + python-h5py + python-lmfit + python-matplotlib + python-networkx + python-numba + python-numpy + python-pandas + python-psutil + python-pysam + python-scikit-learn + python-seaborn + python-tqdm + ;; drep is needed for deprecated plot utilities + python-drep)) + (native-inputs + (list python-pytest)) (home-page "https://github.com/MrOlm/inStrain") (synopsis "Calculation of strain-level metrics") (description @@ -12359,9 +12095,9 @@ allowing the insertion of arbitrary types into the tree.") (setenv "PY_IGNORE_IMPORTMISMATCH" "1") #t))))) (propagated-inputs - `(("python-sortedcontainers" ,python-sortedcontainers))) + (list python-sortedcontainers)) (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/chaimleib/intervaltree") (synopsis "Editable interval tree data structure") (description @@ -12401,7 +12137,7 @@ bound.") "/bin")) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/4dn-dcic/pairix") (synopsis "Support for querying pairix-indexed bgzipped text files") (description @@ -12422,7 +12158,7 @@ bgzipped text file that contains a pair of genomic coordinates per line.") "038xi3a6zvrxbyyfpp64ka8pcjgsdq4fgw9cl5lpxbvmm1bzzw2q")))) (build-system python-build-system) (propagated-inputs - `(("python-six" ,python-six))) + (list python-six)) (home-page "http://mattshirley.com") (synopsis "Random access to fasta subsequences") (description @@ -12470,29 +12206,26 @@ fasta subsequences.") (when tests? (invoke "python" "-m" "pytest" "-v"))))))) (propagated-inputs - `(("python-asciitree" ,python-asciitree) - ("python-biopython" ,python-biopython) - ("python-click" ,python-click) - ("python-cytoolz" ,python-cytoolz-for-cooler) - ("python-dask" ,python-dask) - ("python-h5py" ,python-h5py) - ("python-multiprocess" ,python-multiprocess) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pyfaidx" ,python-pyfaidx) - ("python-pypairix" ,python-pypairix) - ("python-pysam" ,python-pysam) - ("python-pyyaml" ,python-pyyaml) - ("python-scipy" ,python-scipy) - ("python-simplejson" ,python-simplejson) - ("python-six" ,python-six) - ("python-sparse" ,python-sparse))) - (native-inputs - `(("python-codecov" ,python-codecov) - ("python-mock" ,python-mock) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-flake8" ,python-pytest-flake8))) + (list python-asciitree + python-biopython + python-click + python-cytoolz-for-cooler + python-dask + python-h5py + python-multiprocess + python-numpy + python-pandas + python-pyfaidx + python-pypairix + python-pysam + python-pyyaml + python-scipy + python-simplejson + python-six + python-sparse)) + (native-inputs + (list python-codecov python-mock python-pytest python-pytest-cov + python-pytest-flake8)) ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella (home-page "https://github.com/open2c/cooler") (synopsis "Sparse binary format for genomic interaction matrices") @@ -12526,14 +12259,14 @@ such as Hi-C contact matrices.") (when tests? (invoke "python" "-m" "pytest" "-v"))))))) (propagated-inputs - `(("python-cooler" ,python-cooler) - ("python-intervaltree" ,python-intervaltree) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-scipy" ,python-scipy) - ("python-tables" ,python-tables))) - (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-cooler + python-intervaltree + python-numpy + python-pandas + python-scipy + python-tables)) + (native-inputs + (list python-pytest)) (home-page "https://github.com/deeptools/HiCMatrix/") (synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks") (description @@ -12566,21 +12299,21 @@ the HiCExplorer and pyGenomeTracks packages.") (("==") ">=")) #t))))) (propagated-inputs - `(("python-biopython" ,python-biopython) - ("python-configparser" ,python-configparser) - ("python-cooler" ,python-cooler) - ("python-future" ,python-future) - ("python-intervaltree" ,python-intervaltree) - ("python-jinja2" ,python-jinja2) - ("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pybigwig" ,python-pybigwig) - ("python-pysam" ,python-pysam) - ("python-scipy" ,python-scipy) - ("python-six" ,python-six) - ("python-tables" ,python-tables) - ("python-unidecode" ,python-unidecode))) + (list python-biopython + python-configparser + python-cooler + python-future + python-intervaltree + python-jinja2 + python-matplotlib + python-numpy + python-pandas + python-pybigwig + python-pysam + python-scipy + python-six + python-tables + python-unidecode)) (home-page "https://hicexplorer.readthedocs.io") (synopsis "Process, analyze and visualize Hi-C data") (description @@ -12617,17 +12350,17 @@ genomic scores), long range contacts and the visualization of viewpoints.") "matplotlib >=3.1.1")) #t))))) (propagated-inputs - `(("python-future" ,python-future) - ("python-gffutils" ,python-gffutils) - ("python-hicmatrix" ,python-hicmatrix) - ("python-intervaltree" ,python-intervaltree) - ("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-pybigwig" ,python-pybigwig) - ("python-pysam" ,python-pysam) - ("python-tqdm" ,python-tqdm))) - (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-future + python-gffutils + python-hicmatrix + python-intervaltree + python-matplotlib + python-numpy + python-pybigwig + python-pysam + python-tqdm)) + (native-inputs + (list python-pytest)) (home-page "https://pygenometracks.readthedocs.io") (synopsis "Program and library to plot beautiful genome browser tracks") (description @@ -12651,10 +12384,7 @@ pyGenomeTracks can make plots with or without Hi-C data.") (build-system python-build-system) (arguments `(#:tests? #false)) ; there are none (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-scipy" ,python-scipy) - ("python-scikit-learn" ,python-scikit-learn))) + (list python-numpy python-pandas python-scipy python-scikit-learn)) (home-page "https://github.com/hiclib/iced") (synopsis "ICE normalization") (description "This is a package for normalizing Hi-C contact counts @@ -12688,11 +12418,8 @@ efficiently.") (list "test_data/hic2cool_0.4.2_single_res.cool" "test_data/hic2cool_0.7.0_multi_res.mcool"))))))) (propagated-inputs - `(("python-cooler" ,python-cooler) - ("python-h5py" ,python-h5py) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-scipy" ,python-scipy))) + (list python-cooler python-h5py python-numpy python-pandas + python-scipy)) (home-page "https://github.com/4dn-dcic/hic2cool") (synopsis "Converter for .hic and .cool files") (description @@ -12717,11 +12444,7 @@ matrices.") (properties `((upstream-name . "poRe"))) (build-system r-build-system) (propagated-inputs - `(("r-bit64" ,r-bit64) - ("r-data-table" ,r-data-table) - ("r-rhdf5" ,r-rhdf5) - ("r-shiny" ,r-shiny) - ("r-svdialogs" ,r-svdialogs))) + (list r-bit64 r-data-table r-rhdf5 r-shiny r-svdialogs)) (home-page "https://sourceforge.net/projects/rpore/") (synopsis "Visualize Nanopore sequencing data") (description @@ -12748,15 +12471,15 @@ sequencing data.") "0w8bsq5myiwkfhh83nm6is5ichiyvwa1axx2szvxnzq39x6knf66")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-assertthat" ,r-assertthat) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-digest" ,r-digest) - ("r-pkgmaker" ,r-pkgmaker) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-stringr" ,r-stringr))) + (list r-annotationdbi + r-assertthat + r-biobase + r-biocmanager + r-digest + r-pkgmaker + r-plyr + r-reshape2 + r-stringr)) (home-page "https://github.com/renozao/xbioc/") (synopsis "Extra base functions for Bioconductor") (description "This package provides extra utility functions to perform @@ -12781,12 +12504,12 @@ provided by Bioconductor packages.") "128syf9v39gk0z3ip000qpsjbg6l1siyq6c8b0hz41dzg5achyb3")))) (build-system r-build-system) (propagated-inputs - `(("r-formula" ,r-formula) - ("r-ggplot2" ,r-ggplot2) - ("r-pkgmaker" ,r-pkgmaker) - ("r-plyr" ,r-plyr) - ("r-rngtools" ,r-rngtools) - ("r-scales" ,r-scales))) + (list r-formula + r-ggplot2 + r-pkgmaker + r-plyr + r-rngtools + r-scales)) (home-page "https://github.com/shenorrLab/csSAM/") (synopsis "Cell type-specific statistical analysis of microarray") (description "This package implements the method csSAM that computes @@ -12812,23 +12535,23 @@ SAM.") "1prw13wa20f7wlc3gkkls66n1kxz8d28qrb8icfqdwdnnv8w5qg8")))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-cssam" ,r-cssam) - ("r-dplyr" ,r-dplyr) - ("r-e1071" ,r-e1071) - ("r-edger" ,r-edger) - ("r-ggplot2" ,r-ggplot2) - ("r-nmf" ,r-nmf) - ("r-openxlsx" ,r-openxlsx) - ("r-pkgmaker" ,r-pkgmaker) - ("r-plyr" ,r-plyr) - ("r-preprocesscore" ,r-preprocesscore) - ("r-rngtools" ,r-rngtools) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-xbioc" ,r-xbioc))) + (list r-abind + r-annotationdbi + r-biobase + r-cssam + r-dplyr + r-e1071 + r-edger + r-ggplot2 + r-nmf + r-openxlsx + r-pkgmaker + r-plyr + r-preprocesscore + r-rngtools + r-scales + r-stringr + r-xbioc)) (home-page "https://github.com/shenorrLab/bseqsc") (synopsis "Deconvolution of bulk sequencing experiments using single cell data") (description "BSeq-sc is a bioinformatics analysis pipeline that @@ -12892,13 +12615,10 @@ Barcoding Kit or Rapid Barcoding Kit.") ;; requires python >=2.7, <3.0, and the same for python dependencies (arguments `(#:python ,python-2)) (inputs - `(("hdf5" ,hdf5))) + (list hdf5)) (propagated-inputs - `(("python-dateutil" ,python2-dateutil) - ("python-h5py" ,python2-h5py) - ("python-matplotlib" ,python2-matplotlib) - ("python-pandas" ,python2-pandas) - ("python-seaborn" ,python2-seaborn))) + (list python2-dateutil python2-h5py python2-matplotlib + python2-pandas python2-seaborn)) (home-page "https://poretools.readthedocs.io") (synopsis "Toolkit for working with nanopore sequencing data") (description @@ -12966,14 +12686,14 @@ of the Hierarchical Data Format (HDF5) standard.") (list "JAMM.sh" "SignalGenerator.sh"))) #t))))) (inputs - `(("bash" ,bash) - ("coreutils" ,coreutils) - ("gawk" ,gawk) - ("perl" ,perl) - ("r-minimal" ,r-minimal) - ;;("r-parallel" ,r-parallel) - ("r-signal" ,r-signal) - ("r-mclust" ,r-mclust))) + (list bash + coreutils + gawk + perl + r-minimal + ;;("r-parallel" ,r-parallel) + r-signal + r-mclust)) (home-page "https://github.com/mahmoudibrahim/JAMM") (synopsis "Peak finder for NGS datasets") (description @@ -13038,63 +12758,59 @@ datasets.") (string-append bin "ngless-" ,version "-bwa")) #t)))))) (inputs - `(("prodigal" ,prodigal) - ("bwa" ,bwa) - ("samtools" ,samtools) - ("minimap2" ,minimap2) - ("ghc-aeson" ,ghc-aeson) - ("ghc-ansi-terminal" ,ghc-ansi-terminal) - ("ghc-async" ,ghc-async) - ("ghc-atomic-write" ,ghc-atomic-write) - ("ghc-bytestring-lexing" ,ghc-bytestring-lexing) - ("ghc-conduit" ,ghc-conduit) - ("ghc-conduit-algorithms" ,ghc-conduit-algorithms) - ("ghc-conduit-extra" ,ghc-conduit-extra) - ("ghc-configurator" ,ghc-configurator) - ("ghc-convertible" ,ghc-convertible) - ("ghc-data-default" ,ghc-data-default) - ("ghc-diagrams-core" ,ghc-diagrams-core) - ("ghc-diagrams-lib" ,ghc-diagrams-lib) - ("ghc-diagrams-svg" ,ghc-diagrams-svg) - ("ghc-double-conversion" ,ghc-double-conversion) - ("ghc-edit-distance" ,ghc-edit-distance) - ("ghc-either" ,ghc-either) - ("ghc-errors" ,ghc-errors) - ("ghc-extra" ,ghc-extra) - ("ghc-filemanip" ,ghc-filemanip) - ("ghc-file-embed" ,ghc-file-embed) - ("ghc-gitrev" ,ghc-gitrev) - ("ghc-hashtables" ,ghc-hashtables) - ("ghc-http-conduit" ,ghc-http-conduit) - ("ghc-inline-c" ,ghc-inline-c) - ("ghc-inline-c-cpp" ,ghc-inline-c-cpp) - ("ghc-int-interval-map" ,ghc-int-interval-map) - ("ghc-missingh" ,ghc-missingh) - ("ghc-optparse-applicative" ,ghc-optparse-applicative) - ("ghc-regex" ,ghc-regex) - ("ghc-safe" ,ghc-safe) - ("ghc-safeio" ,ghc-safeio) - ("ghc-strict" ,ghc-strict) - ("ghc-tar" ,ghc-tar) - ("ghc-tar-conduit" ,ghc-tar-conduit) - ("ghc-unliftio" ,ghc-unliftio) - ("ghc-unliftio-core" ,ghc-unliftio-core) - ("ghc-vector" ,ghc-vector) - ("ghc-yaml" ,ghc-yaml) - ("ghc-zlib" ,ghc-zlib))) + (list prodigal + bwa + samtools + minimap2 + ghc-aeson + ghc-ansi-terminal + ghc-async + ghc-atomic-write + ghc-bytestring-lexing + ghc-conduit + ghc-conduit-algorithms + ghc-conduit-extra + ghc-configurator + ghc-convertible + ghc-data-default + ghc-diagrams-core + ghc-diagrams-lib + ghc-diagrams-svg + ghc-double-conversion + ghc-edit-distance + ghc-either + ghc-errors + ghc-extra + ghc-filemanip + ghc-file-embed + ghc-gitrev + ghc-hashtables + ghc-http-conduit + ghc-inline-c + ghc-inline-c-cpp + ghc-int-interval-map + ghc-missingh + ghc-optparse-applicative + ghc-regex + ghc-safe + ghc-safeio + ghc-strict + ghc-tar + ghc-tar-conduit + ghc-unliftio + ghc-unliftio-core + ghc-vector + ghc-yaml + ghc-zlib)) (propagated-inputs - `(("r-r6" ,r-r6) - ("r-hdf5r" ,r-hdf5r) - ("r-iterators" ,r-iterators) - ("r-itertools" ,r-itertools) - ("r-matrix" ,r-matrix))) - (native-inputs - `(("ghc-hpack" ,ghc-hpack) - ("ghc-quickcheck" ,ghc-quickcheck) - ("ghc-test-framework" ,ghc-test-framework) - ("ghc-test-framework-hunit",ghc-test-framework-hunit) - ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2) - ("ghc-test-framework-th" ,ghc-test-framework-th))) + (list r-r6 r-hdf5r r-iterators r-itertools r-matrix)) + (native-inputs + (list ghc-hpack + ghc-quickcheck + ghc-test-framework + ghc-test-framework-hunit + ghc-test-framework-quickcheck2 + ghc-test-framework-th)) (home-page "https://ngless.embl.de/") (synopsis "DSL for processing next-generation sequencing data") (description "Ngless is a domain-specific language for @@ -13117,17 +12833,14 @@ datasets.") (sha256 (base32 "0fd728b5if89vj5j4f9y7k0b2xv2ycz5a21iy15wbdcf5bhim7i8")))) (build-system haskell-build-system) (inputs - `(("ghc-either" ,ghc-either) - ("ghc-primitive" ,ghc-primitive) - ("ghc-vector" ,ghc-vector) - ("ghc-vector-algorithms" ,ghc-vector-algorithms))) + (list ghc-either ghc-primitive ghc-vector ghc-vector-algorithms)) (native-inputs - `(("ghc-hedgehog" ,ghc-hedgehog) - ("ghc-tasty" ,ghc-tasty) - ("ghc-tasty-hedgehog" ,ghc-tasty-hedgehog) - ("ghc-tasty-hunit" ,ghc-tasty-hunit) - ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck) - ("ghc-tasty-th" ,ghc-tasty-th))) + (list ghc-hedgehog + ghc-tasty + ghc-tasty-hedgehog + ghc-tasty-hunit + ghc-tasty-quickcheck + ghc-tasty-th)) (home-page "https://github.com/luispedro/interval-to-int#readme") (synopsis "Interval map structure in Haskell") (description "An interval map structure that is optimized for low @@ -13300,17 +13013,17 @@ polymorphisms) and indels with respect to a reference genome and more.") (base32 "0g2f78k68yglmj4fsfmgs8idqv3di9aj53fg0ld0hqljg8chhh82")))) (build-system python-build-system) (propagated-inputs - `(("python-biopython" ,python-biopython) - ("python-future" ,python-future) - ("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-reportlab" ,python-reportlab) - ("python-pandas" ,python-pandas) - ("python-pysam" ,python-pysam) - ("python-pyfaidx" ,python-pyfaidx) - ("python-scipy" ,python-scipy) - ;; R packages - ("r-dnacopy" ,r-dnacopy))) + (list python-biopython + python-future + python-matplotlib + python-numpy + python-reportlab + python-pandas + python-pysam + python-pyfaidx + python-scipy + ;; R packages + r-dnacopy)) (home-page "https://cnvkit.readthedocs.org/") (synopsis "Copy number variant detection from targeted DNA sequencing") (description @@ -13337,11 +13050,11 @@ Torrent.") (build-system python-build-system) (arguments '(#:tests? #false)) ; there are none (propagated-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (inputs - `(("fftw" ,fftw))) + (list fftw)) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (home-page "https://github.com/KlugerLab/pyFIt-SNE") (synopsis "FFT-accelerated Interpolation-based t-SNE") (description @@ -13410,10 +13123,8 @@ is a Cython wrapper for FIt-SNE.") #t))) #:jdk ,openjdk11)) (inputs - `(("gawk" ,gawk) - ("java-eclipse-jdt-core" ,java-eclipse-jdt-core) - ("java-eclipse-jdt-compiler-apt" ,java-eclipse-jdt-compiler-apt) - ("java-openmpi" ,java-openmpi))) + (list gawk java-eclipse-jdt-core java-eclipse-jdt-compiler-apt + java-openmpi)) (home-page "https://sourceforge.net/projects/bbmap/") (synopsis "Aligner and other tools for short sequencing reads") (description @@ -13468,8 +13179,7 @@ to an artifact/contaminant file.") (install-file "Manual.pdf" doc) (install-file "Columbus_manual.pdf" doc))))))) (inputs - `(("openmpi" ,openmpi) - ("zlib" ,zlib))) + (list openmpi zlib)) (native-inputs `(("texlive" ,(texlive-updmap.cfg (list texlive-latex-graphics texlive-fonts-ec @@ -13501,19 +13211,19 @@ repeated areas between contigs.") '(for-each delete-file (find-files "." "\\.c"))))) (build-system python-build-system) (native-inputs - `(("python-joblib" ,python-joblib))) + (list python-joblib)) (propagated-inputs - `(("python-click" ,python-click) - ("python-cython" ,python-cython) - ("python-h5py" ,python-h5py) - ("python-loompy" ,python-loompy) - ("python-matplotlib" ,python-matplotlib) - ("python-numba" ,python-numba) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pysam" ,python-pysam) - ("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy))) + (list python-click + python-cython + python-h5py + python-loompy + python-matplotlib + python-numba + python-numpy + python-pandas + python-pysam + python-scikit-learn + python-scipy)) (home-page "https://github.com/velocyto-team/velocyto.py") (synopsis "RNA velocity analysis for single cell RNA-seq data") (description @@ -13565,14 +13275,14 @@ includes a command line tool and an analysis pipeline.") `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))) #t))))) (inputs - `(("htslib" ,htslib) - ("r-minimal" ,r-minimal) - ("r-circlize" ,r-circlize) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("samtools" ,samtools) - ("star" ,star) - ("zlib" ,zlib))) + (list htslib + r-minimal + r-circlize + r-genomicalignments + r-genomicranges + samtools + star + zlib)) (home-page "https://github.com/suhrig/arriba") (synopsis "Gene fusion detection from RNA-Seq data ") (description @@ -13611,7 +13321,7 @@ tools which build on STAR, Arriba does not require to reduce the (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://adapterremoval.readthedocs.io/") (synopsis "Rapid sequence adapter trimming, identification, and read merging") (description @@ -13730,7 +13440,7 @@ let before_space s = ("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild)) ("pkg-config" ,pkg-config))) (propagated-inputs - `(("pplacer-scripts" ,pplacer-scripts))) + (list pplacer-scripts)) (synopsis "Phylogenetic placement of biological sequences") (description "Pplacer places query sequences on a fixed reference phylogenetic tree @@ -13800,11 +13510,8 @@ downstream analysis.") (lambda _ (setenv "HOME" "/tmp")))))) (inputs - `(("python-dendropy" ,python-dendropy) - ("python-matplotlib" ,python-matplotlib) - ("python-numpy" ,python-numpy) - ("python-pysam" ,python-pysam) - ("python-scipy" ,python-scipy))) + (list python-dendropy python-matplotlib python-numpy python-pysam + python-scipy)) (home-page "https://ecogenomics.github.io/CheckM/") (synopsis "Assess the quality of putative genome bins") (description @@ -13836,14 +13543,14 @@ proximity within a reference genome.") "08y3vz1vcx09whmbsn722lcs6jl9wyrh9i4p3k8j4cb1i32bij4a")))) (build-system python-build-system) (inputs - `(("python-pandas" ,python-pandas) - ("python-future" ,python-future) - ("python-scipy" ,python-scipy) - ("python-matplotlib" ,python-matplotlib) - ("python-regex" ,python-regex) - ("python-pysam" ,python-pysam))) + (list python-pandas + python-future + python-scipy + python-matplotlib + python-regex + python-pysam)) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (home-page "https://github.com/CGATOxford/UMI-tools") (synopsis "Tools for analyzing unique modular identifiers") (description "This package provides tools for dealing with @dfn{Unique @@ -13883,12 +13590,9 @@ on the needs of the user.") (modify-phases %standard-phases (delete 'configure)))) (inputs - `(("boost" ,boost) - ("htslib" ,htslib) - ("ncurses" ,ncurses) - ("zlib" ,zlib))) + (list boost htslib ncurses zlib)) (native-inputs - `(("lcov" ,lcov))) + (list lcov)) (home-page "https://github.com/ParkerLab/ataqv") (synopsis "Toolkit for quality control and visualization of ATAC-seq data") (description "This package provides a toolkit for measuring and comparing @@ -13912,13 +13616,13 @@ might be caused by ATAC-seq library prep or sequencing. The main program, (base32 "08438h16cfry5kqh3y9hs8q1b1a8bxhblsm75knviz5r6q0n1jxh")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-dplyr" ,r-dplyr) - ("r-tidyr" ,r-tidyr) - ("r-purrr" ,r-purrr) - ("r-readr" ,r-readr) - ("r-magrittr" ,r-magrittr) - ("r-ggplot2" ,r-ggplot2))) + (list r-mass + r-dplyr + r-tidyr + r-purrr + r-readr + r-magrittr + r-ggplot2)) (home-page "https://github.com/kcha/psiplot") (synopsis "Plot percent spliced-in values of alternatively-spliced exons") (description @@ -13952,10 +13656,10 @@ are generated using @code{ggplot2}.") ;; disable building them. "-DENABLE_PYTHON=OFF"))) (inputs - `(;("hdf5" ,hdf5-1.10) - ("zstd" ,zstd "lib"))) + (list ;("hdf5" ,hdf5-1.10) + `(,zstd "lib"))) (native-inputs - `(("googlebenchmark" ,googlebenchmark))) + (list googlebenchmark)) (home-page "https://github.com/nanoporetech/vbz_compression/") (synopsis "VBZ compression plugin for nanopore signal data") (description @@ -13994,12 +13698,9 @@ effective when applied to the signal dataset.") "/hdf5/lib/plugin/libvbz_hdf_plugin.so") "ont_fast5_api/vbz_plugin/")))))) (inputs - `(("vbz-compression" ,vbz-compression))) + (list vbz-compression)) (propagated-inputs - `(("python-numpy" ,python-numpy) - ("python-h5py" ,python-h5py) - ("python-packaging" ,python-packaging) - ("python-progressbar33" ,python-progressbar33))) + (list python-numpy python-h5py python-packaging python-progressbar33)) (home-page "https://github.com/nanoporetech/ont_fast5_api") (synopsis "Interface to HDF5 files of the Oxford Nanopore fast5 file format") (description @@ -14035,13 +13736,13 @@ and reflect the fast5 file schema, and tools to convert between (substitute* "setup.py" ((", <3.0") ""))))))) ; matplotlib (inputs - `(("python-matplotlib" ,python-matplotlib) - ("python-networkx" ,python-networkx) - ("python-numpy" ,python-numpy) - ("python-pybigwig" ,python-pybigwig) - ("python-biopython" ,python-biopython-1.73) - ("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy))) + (list python-matplotlib + python-networkx + python-numpy + python-pybigwig + python-biopython-1.73 + python-scikit-learn + python-scipy)) (home-page "https://github.com/phoenixding/tbsp/") (synopsis "SNP-based trajectory inference") (description @@ -14072,8 +13773,7 @@ mutations from scRNA-Seq data.") (delete-file-recursively "htslib") #t)))) (build-system gnu-build-system) (inputs - `(("htslib" ,htslib) - ("zlib" ,zlib))) + (list htslib zlib)) (arguments `(#:tests? #f ; There are no tests to run. #:phases @@ -14249,7 +13949,7 @@ combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "fsom" bin))))))) (native-inputs - `(("gcc" ,gcc-6))) + (list gcc-6)) (home-page "https://github.com/ekg/fsom") (synopsis "Manage SOM (Self-Organizing Maps) neural networks") (description "A tiny C library for managing SOM (Self-Organizing Maps) @@ -14360,15 +14060,15 @@ library automatically handles index file generation and use.") #t)))) (build-system cmake-build-system) (inputs - `(("bzip2" ,bzip2) - ("htslib" ,htslib) - ("fastahack" ,fastahack) - ("perl" ,perl) - ("python" ,python) - ("smithwaterman" ,smithwaterman) - ("tabixpp" ,tabixpp) - ("xz" ,xz) - ("zlib" ,zlib))) + (list bzip2 + htslib + fastahack + perl + python + smithwaterman + tabixpp + xz + zlib)) (native-inputs `(("pkg-config" ,pkg-config) ;; Submodules. @@ -14453,11 +14153,7 @@ manipulations on VCF files.") #t)))) (build-system meson-build-system) (inputs - `(("fastahack" ,fastahack) - ("htslib" ,htslib) - ("smithwaterman" ,smithwaterman) - ("tabixpp" ,tabixpp) - ("vcflib" ,vcflib))) + (list fastahack htslib smithwaterman tabixpp vcflib)) (native-inputs `(("bash-tap" ,bash-tap) ("bc" ,bc) @@ -14574,24 +14270,24 @@ pairs.") "16wqf70j7rd7pay2q513iyz12i8n9vrpg1bisah4lddbcpx5dz1n")))) (build-system r-build-system) (inputs - `(("boost" ,boost))) + (list boost)) (propagated-inputs - `(("r-hdf5r" ,r-hdf5r) - ("r-mass" ,r-mass) - ("r-mgcv" ,r-mgcv) - ("r-pcamethods" ,r-pcamethods) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ;; Suggested packages - ("r-rtsne" ,r-rtsne) - ("r-cluster" ,r-cluster) - ("r-abind" ,r-abind) - ("r-h5" ,r-h5) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicalignments" ,r-genomicalignments) - ("r-rsamtools" ,r-rsamtools) - ("r-edger" ,r-edger) - ("r-igraph" ,r-igraph))) + (list r-hdf5r + r-mass + r-mgcv + r-pcamethods + r-rcpp + r-rcpparmadillo + ;; Suggested packages + r-rtsne + r-cluster + r-abind + r-h5 + r-biocgenerics + r-genomicalignments + r-rsamtools + r-edger + r-igraph)) (home-page "https://velocyto.org") (synopsis "RNA velocity estimation in R") (description @@ -14629,10 +14325,8 @@ patterns.") (("install MethylDackel \\$\\(prefix\\)" match) (string-append "install -d $(prefix); " match)))))))) (inputs - `(("curl" ,curl) ; XXX: needed by libbigwig - ("htslib" ,htslib-1.9) - ("libbigwig" ,libbigwig) - ("zlib" ,zlib))) + (list curl ; XXX: needed by libbigwig + htslib-1.9 libbigwig zlib)) ;; Needed for tests (native-inputs `(("python" ,python-wrapper))) @@ -14702,9 +14396,9 @@ containing the reference genome as well.") ;; unknown reasons. (invoke "make" "-C" "test" "msa_view")))))) (inputs - `(("clapack" ,clapack))) + (list clapack)) (native-inputs - `(("perl" ,perl))) + (list perl)) (home-page "http://compgen.cshl.edu/phast/") (synopsis "Phylogenetic analysis with space/time models") (description @@ -14749,15 +14443,15 @@ alignments, trees and genomic annotations.") (find-files "." "\\.gz")) #t))))) (propagated-inputs - `(("python-argcomplete" ,python-argcomplete) - ("python-argh" ,python-argh) - ("python-biopython" ,python-biopython) - ("python-pybedtools" ,python-pybedtools) - ("python-pyfaidx" ,python-pyfaidx) - ("python-simplejson" ,python-simplejson) - ("python-six" ,python-six))) + (list python-argcomplete + python-argh + python-biopython + python-pybedtools + python-pyfaidx + python-simplejson + python-six)) (native-inputs - `(("python-nose" , python-nose))) + (list python-nose)) (home-page "https://github.com/daler/gffutils") (synopsis "Tool for manipulation of GFF and GTF files") (description @@ -14790,7 +14484,7 @@ than is possible with plain-text methods alone.") `(("java-commons-lang2" ,java-commons-lang) ("java-args4j" ,java-args4j))) (native-inputs - `(("java-junit" ,java-junit))) + (list java-junit)) (home-page "https://github.com/cbg-ethz/InDelFixer/") (synopsis "Iterative and sensitive NGS sequence aligner") (description "InDelFixer is a sensitive aligner for 454, Illumina and @@ -14827,10 +14521,9 @@ The output is in SAM format.") #$(this-package-input "libxml2") "/include/libxml2")))) (propagated-inputs - `(("libxml2" ,libxml2))) + (list libxml2)) (native-inputs - `(("check" ,check-0.14) - ("swig" ,swig))) + (list check-0.14 swig)) (home-page "http://sbml.org/Software/libSBML") (synopsis "Process SBML files and data streams") (description "LibSBML is a library to help you read, write, manipulate, @@ -14915,12 +14608,12 @@ international community.") (install-file script bin)) scripts))))))))) (inputs - `(("gzip" ,gzip) - ("perl" ,perl) - ("rsync" ,rsync) - ("sed" ,sed) - ("wget" ,wget) - ("which" ,which))) + (list gzip + perl + rsync + sed + wget + which)) (home-page "https://github.com/DerrickWood/kraken2") (synopsis "Taxonomic sequence classification system") (description "Kraken is a taxonomic sequence classifier that assigns @@ -14952,9 +14645,7 @@ genomes known to contain a given k-mer.") ("python" ,python-wrapper) ("zlib" ,zlib))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("which" ,which))) + (list autoconf automake which)) (home-page "https://csb5.github.io/lofreq/") (synopsis "Sensitive variant calling from sequencing data ") (description "LoFreq is a fast and sensitive variant-caller for inferring @@ -14980,11 +14671,9 @@ usually ignored by other methods or only used for filtering.") (build-system gnu-build-system) (arguments `(#:parallel-tests? #false)) ; not supported (inputs - `(("htslib" ,htslib) - ("zlib" ,zlib))) + (list htslib zlib)) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake))) + (list autoconf automake)) (home-page "https://andersen-lab.github.io/ivar/html/") (synopsis "Tools for amplicon-based sequencing") (description "iVar is a computational package that contains functions @@ -15008,7 +14697,7 @@ broadly useful for viral amplicon-based sequencing. ") (build-system python-build-system) (arguments `(#:tests? #false)) ; the tests access the web (native-inputs - `(("python-pytest" ,python-pytest))) + (list python-pytest)) (home-page "https://github.com/konstantint/pyliftover") (synopsis "Python implementation of UCSC liftOver genome coordinate conversion") (description @@ -15055,15 +14744,15 @@ coordinates between different assemblies.") ("hostname" ,inetutils) ("openssl" ,openssl))) (inputs - `(("time" ,time))) + (list time)) (propagated-inputs - `(("python-apsw" ,python-apsw) - ("python-gevent" ,python-gevent) - ("python-pandas" ,python-pandas) - ("python-paramiko" ,python-paramiko) - ("python-pyyaml" ,python-pyyaml) - ("python-ruffus" ,python-ruffus) - ("python-sqlalchemy" ,python-sqlalchemy))) + (list python-apsw + python-gevent + python-pandas + python-paramiko + python-pyyaml + python-ruffus + python-sqlalchemy)) (home-page "https://github.com/cgat-developers/cgat-core") (synopsis "Computational genomics analysis toolkit") (description @@ -15159,7 +14848,7 @@ large-scale data-analysis.") ("python-scikit-learn" ,python-scikit-learn) ("r-minimal" ,r-minimal))) (native-inputs - `(("perl-module-build" ,perl-module-build))) + (list perl-module-build)) (home-page "https://github.com/dekkerlab/cworld-dekker") (synopsis "Utility and analysis scripts for 3C, 4C, 5C, and Hi-C data") (description "This package is a collection of Perl, Python, and R @@ -15275,16 +14964,16 @@ my @test_files = map {\"$dirname\\/t\\/\".$_} grep {!/^\\./ && /\\.t$/} readdir runtests(@test_files); ")))))))) (inputs - `(("bioperl-minimal" ,bioperl-minimal) - ("perl-bio-db-hts" ,perl-bio-db-hts) - ("perl-dbi" ,perl-dbi) - ("perl-dbd-mysql" ,perl-dbd-mysql) - ("perl-libwww" ,perl-libwww) - ("perl-http-tiny" ,perl-http-tiny) - ("perl-json" ,perl-json) - ("which" ,which))) + (list bioperl-minimal + perl-bio-db-hts + perl-dbi + perl-dbd-mysql + perl-libwww + perl-http-tiny + perl-json + which)) (propagated-inputs - `(("kentutils" ,kentutils))) + (list kentutils)) (native-inputs `(("unzip" ,unzip) ("perl" ,perl) @@ -15330,39 +15019,39 @@ translates between different variant encodings.") "1yihhrv7zs87ax61la1nb4y12lg3knraw4b20k5digbcwm8488lb")))) (properties `((upstream-name . "Signac"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-annotationfilter" ,r-annotationfilter) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-fastmatch" ,r-fastmatch) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggforce" ,r-ggforce) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggseqlogo" ,r-ggseqlogo) - ("r-iranges" ,r-iranges) - ("r-irlba" ,r-irlba) - ("r-lsa" ,r-lsa) - ("r-matrix" ,r-matrix) - ("r-patchwork" ,r-patchwork) - ("r-pbapply" ,r-pbapply) - ("r-rcpp" ,r-rcpp) - ("r-rcpproll" ,r-rcpproll) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-seurat" ,r-seurat) - ("r-seuratobject" ,r-seuratobject) - ("r-stringi" ,r-stringi) - ("r-tidyr" ,r-tidyr))) + (list r-annotationfilter + r-biocgenerics + r-biostrings + r-biovizbase + r-data-table + r-dplyr + r-fastmatch + r-future + r-future-apply + r-genomeinfodb + r-genomicranges + r-ggbio + r-ggforce + r-ggplot2 + r-ggrepel + r-ggseqlogo + r-iranges + r-irlba + r-lsa + r-matrix + r-patchwork + r-pbapply + r-rcpp + r-rcpproll + r-rsamtools + r-s4vectors + r-scales + r-seurat + r-seuratobject + r-stringi + r-tidyr)) (home-page "https://github.com/timoast/signac/") (synopsis "Analysis of single-cell chromatin data") (description @@ -15386,18 +15075,17 @@ sequence motif analysis.") "1023hadgcsgi53kz53ql45207hfizf9sw57z0qij3ay1bx68zbpm")))) (build-system python-build-system) (native-inputs - `(("python-cython" ,python-cython) - ("python-nose2" ,python-nose2))) + (list python-cython python-nose2)) ;; The package mainly consists of a command-line tool, but also has a ;; Python-API. Thus these must be propagated. (propagated-inputs - `(("python-future" ,python-future) - ("python-h5py" ,python-h5py) - ("python-mappy" ,python-mappy) - ("python-numpy" ,python-numpy) - ("python-scipy" ,python-scipy) - ("python-tqdm" ,python-tqdm) - ("python-rpy2" ,python-rpy2))) + (list python-future + python-h5py + python-mappy + python-numpy + python-scipy + python-tqdm + python-rpy2)) (home-page "https://github.com/nanoporetech/tombo") (synopsis "Analysis of raw nanopore sequencing data") (description "Tombo is a suite of tools primarily for the identification of @@ -15438,10 +15126,9 @@ for the analysis and visualization of raw nanopore signal.") (delete-file-recursively (string-append (site-packages inputs outputs) "/vcf/test"))))))) - (native-inputs `(("python-cython" ,python-cython))) + (native-inputs (list python-cython)) (propagated-inputs - `(("python-pysam" ,python-pysam) - ("python-rpy2" ,python-rpy2))) + (list python-pysam python-rpy2)) (home-page "https://github.com/jamescasbon/PyVCF") (synopsis "Variant Call Format parser for Python") (description "This package provides a @acronym{VCF,Variant Call Format} @@ -15460,9 +15147,7 @@ parser for Python.") "1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg")))) (build-system python-build-system) (inputs - `(("python-configparser" ,python-configparser) - ("python-pysam" ,python-pysam) - ("python-pyvcf" ,python-pyvcf))) + (list python-configparser python-pysam python-pyvcf)) (home-page "https://github.com/mroosmalen/nanosv") (synopsis "Structural variation detection tool for Oxford Nanopore data.") (description "NanoSV is a software package that can be used to identify @@ -15484,10 +15169,9 @@ instruments, or Pacific Biosciences RSII or Sequel sequencers.") "1z1gy8n56lhriy6hdkh9r82ndikndipq2cy2wh8q185qig4rimr6")))) (build-system python-build-system) (inputs - `(("curl" ,curl) - ("zlib" ,zlib))) + (list curl zlib)) (propagated-inputs - `(("pybind11" ,pybind11))) + (list pybind11)) (home-page "https://github.com/aidenlab/straw") (synopsis "Stream data from .hic files") (description "Straw is library which allows rapid streaming of contact @@ -15520,18 +15204,11 @@ data from @file{.hic} files. This package provides Python bindings.") (with-directory-excursion "/tmp/tests" (invoke "python" "-m" "pytest" "-v")))))))) (native-inputs - `(("pkg-config" ,pkg-config) - ("python-pkgconfig" ,python-pkgconfig) - ("python-pytest" ,python-pytest))) + (list pkg-config python-pkgconfig python-pytest)) (inputs - `(("libpng" ,libpng) - ("openssl" ,openssl) - ("zlib" ,zlib))) + (list libpng openssl zlib)) (propagated-inputs - `(("python-cython" ,python-cython) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-six" ,python-six))) + (list python-cython python-numpy python-pandas python-six)) (home-page "https://github.com/nvictus/pybbi") (synopsis "Python bindings to UCSC Big Binary file library") (description @@ -15555,8 +15232,7 @@ feature is fast retrieval of range queries into numpy arrays.") (build-system python-build-system) (arguments '(#:tests? #false)) ; there are none (propagated-inputs - `(("python-biopython" ,python-biopython) - ("python-matplotlib" ,python-matplotlib))) + (list python-biopython python-matplotlib)) (home-page "https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer") (synopsis "Plot features from DNA sequences") @@ -15579,28 +15255,28 @@ e.g. from GenBank or Gff files, or Biopython SeqRecords.") (build-system python-build-system) (arguments '(#:tests? #false)) ; there are none (inputs - `(("pybind11" ,pybind11))) + (list pybind11)) (propagated-inputs - `(("python-cooler" ,python-cooler) - ("python-dna-features-viewer" ,python-dna-features-viewer) - ("python-fire" ,python-fire) - ("python-h5py" ,python-h5py) - ("python-intervaltree" ,python-intervaltree) - ("python-ipywidgets" ,python-ipywidgets) - ("jupyter" ,jupyter) - ("python-matplotlib" ,python-matplotlib) - ("python-nbformat" ,python-nbformat) - ("python-numpy" ,python-numpy) - ("python-numpydoc" ,python-numpydoc) - ("python-pandas" ,python-pandas) - ("python-pybbi" ,python-pybbi) - ("python-pytest" ,python-pytest) - ("python-scipy" ,python-scipy) - ("python-statsmodels" ,python-statsmodels) - ("python-strawc" ,python-strawc) - ("python-svgutils" ,python-svgutils) - ("python-termcolor" ,python-termcolor) - ("python-voila" ,python-voila))) + (list python-cooler + python-dna-features-viewer + python-fire + python-h5py + python-intervaltree + python-ipywidgets + jupyter + python-matplotlib + python-nbformat + python-numpy + python-numpydoc + python-pandas + python-pybbi + python-pytest + python-scipy + python-statsmodels + python-strawc + python-svgutils + python-termcolor + python-voila)) (home-page "https://github.com/GangCaoLab/CoolBox") (synopsis "Genomic data visualization toolkit") (description @@ -15648,7 +15324,7 @@ browser.") (add-installed-pythonpath inputs outputs) (invoke "python" "tests/test_pyspoa.py"))))))) (propagated-inputs - `(("pybind11" ,pybind11))) + (list pybind11)) (native-inputs `(("cmake" ,cmake-minimal))) (home-page "https://github.com/nanoporetech/pyspoa") @@ -15685,11 +15361,9 @@ sequences") ;; problem with the C sources. (delete 'sanity-check)))) (propagated-inputs - `(("python-cffi" ,python-cffi) - ("python-setuptools" ,python-setuptools) - ("python-wheel" ,python-wheel))) + (list python-cffi python-setuptools python-wheel)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/ACEnglish/bwapy") (synopsis "Python bindings to bwa alinger") (description "This package provides Python bindings to the bwa mem @@ -15722,21 +15396,21 @@ aligner.") (substitute* "setup.py" (("'sklearn',") ""))))))) (native-inputs - `(("python-cython" ,python-cython))) + (list python-cython)) (propagated-inputs - `(("python-scikit-learn" ,python-scikit-learn) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-hmmlearn" ,python-hmmlearn) - ("python-pandas" ,python-pandas) - ("python-numba" ,python-numba) - ("python-anndata" ,python-anndata) - ("python-scanpy" ,python-scanpy) - ("python-pybedtools" ,python-pybedtools) - ("python-pysam" ,python-pysam) - ("python-matplotlib" ,python-matplotlib) - ("python-seaborn" ,python-seaborn) - ("python-coolbox" ,python-coolbox))) + (list python-scikit-learn + python-scipy + python-numpy + python-hmmlearn + python-pandas + python-numba + python-anndata + python-scanpy + python-pybedtools + python-pysam + python-matplotlib + python-seaborn + python-coolbox)) (home-page "https://github.com/BIMSBbioinfo/scregseg") (synopsis "Single-cell regulatory landscape segmentation") (description "Scregseg (Single-Cell REGulatory landscape SEGmentation) is a @@ -15795,15 +15469,9 @@ cross-cluster accessibility profiles.") (copy-file "megadepth_dynamic" (string-append bin "/megadepth")))))))) (native-inputs - `(("diffutils" ,diffutils) - ("perl" ,perl) - ("grep" ,grep))) + (list diffutils perl grep)) (inputs - `(("curl" ,curl) - ("htslib" ,htslib) - ("libdeflate" ,libdeflate) - ("libbigwig" ,libbigwig) - ("zlib" ,zlib))) + (list curl htslib libdeflate libbigwig zlib)) (home-page "https://github.com/ChristopherWilks/megadepth") (synopsis "BigWig and BAM/CRAM related utilities") (description "Megadepth is an efficient tool for extracting coverage @@ -15834,7 +15502,7 @@ both types of files.") (lambda _ (chdir "ASCAT")))))) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-rcolorbrewer)) (home-page "https://github.com/VanLoo-lab/ascat/") (synopsis "Allele-Specific Copy Number Analysis of Tumors in R") (description "This package provides the @acronym{ASCAT,Allele-Specific Copy @@ -15857,14 +15525,14 @@ ploidy and allele-specific copy number profiles.") "0nmcq4c7y5g8h8lxsq9vadz9bj4qgqn118alip520ny6czaxki4h")))) (build-system r-build-system) (propagated-inputs - `(("r-devtools" ,r-devtools) - ("r-readr" ,r-readr) - ("r-doparallel" ,r-doparallel) - ("r-ggplot2" ,r-ggplot2) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-gridextra" ,r-gridextra) - ("r-gtools" ,r-gtools) - ("r-ascat" ,r-ascat))) + (list r-devtools + r-readr + r-doparallel + r-ggplot2 + r-rcolorbrewer + r-gridextra + r-gtools + r-ascat)) (home-page "https://github.com/Wedge-lab/battenberg") (synopsis "Subclonal copy number estimation in R") (description "This package contains the Battenberg R package for subclonal @@ -15919,51 +15587,51 @@ value of physical insulation between neighboring domains.") (properties `((upstream-name . "Spectre"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-caret" ,r-caret) - ("r-class" ,r-class) - ("r-colorramps" ,r-colorramps) - ("r-data-table" ,r-data-table) - ("r-devtools" ,r-devtools) - ("r-dplyr" ,r-dplyr) - ("r-exactextractr" ,r-exactextractr) - ("r-factoextra" ,r-factoextra) - ("r-flowcore" ,r-flowcore) - ("r-flowsom" ,r-flowsom) - ("r-flowviz" ,r-flowviz) - ("r-fnn" ,r-fnn) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpointdensity" ,r-ggpointdensity) - ("r-ggpubr" ,r-ggpubr) - ("r-ggraph" ,r-ggraph) - ("r-ggthemes" ,r-ggthemes) - ("r-gridextra" ,r-gridextra) - ("r-gridextra" ,r-gridextra) - ("r-gtools" ,r-gtools) - ("r-hdf5array" ,r-hdf5array) - ("r-irlba" ,r-irlba) - ("r-pheatmap" ,r-pheatmap) - ("r-plyr" ,r-plyr) - ("r-qs" ,r-qs) - ("r-raster" ,r-raster) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rgeos" ,r-rgeos) - ("r-rhdf5" ,r-rhdf5) - ("r-rstudioapi" ,r-rstudioapi) - ("r-rsvd" ,r-rsvd) - ("r-rtsne" ,r-rtsne) - ("r-s2" ,r-s2) - ("r-scales" ,r-scales) - ("r-sf" ,r-sf) - ("r-sp" ,r-sp) - ("r-stars" ,r-stars) - ("r-stringr" ,r-stringr) - ("r-tidygraph" ,r-tidygraph) - ("r-tidyr" ,r-tidyr) - ("r-tidyr" ,r-tidyr) - ("r-tiff" ,r-tiff) - ("r-umap" ,r-umap))) + (list r-biobase + r-biocmanager + r-caret + r-class + r-colorramps + r-data-table + r-devtools + r-dplyr + r-exactextractr + r-factoextra + r-flowcore + r-flowsom + r-flowviz + r-fnn + r-ggplot2 + r-ggpointdensity + r-ggpubr + r-ggraph + r-ggthemes + r-gridextra + r-gridextra + r-gtools + r-hdf5array + r-irlba + r-pheatmap + r-plyr + r-qs + r-raster + r-rcolorbrewer + r-rgeos + r-rhdf5 + r-rstudioapi + r-rsvd + r-rtsne + r-s2 + r-scales + r-sf + r-sp + r-stars + r-stringr + r-tidygraph + r-tidyr + r-tidyr + r-tiff + r-umap)) (home-page "https://github.com/ImmuneDynamics/Spectre") (synopsis "High-dimensional cytometry and imaging analysis") (description @@ -15991,16 +15659,16 @@ cytometry and imaging data.") (properties `((upstream-name . "CytoNorm"))) (build-system r-build-system) (propagated-inputs - `(("r-cytoml" ,r-cytoml) - ("r-dplyr" ,r-dplyr) - ("r-emdist" ,r-emdist) - ("r-flowcore" ,r-flowcore) - ("r-flowsom" ,r-flowsom) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-pheatmap" ,r-pheatmap) - ("r-stringr" ,r-stringr))) + (list r-cytoml + r-dplyr + r-emdist + r-flowcore + r-flowsom + r-flowworkspace + r-ggplot2 + r-gridextra + r-pheatmap + r-stringr)) (home-page "https://github.com/saeyslab/CytoNorm") (synopsis "Normalize cytometry data measured across multiple batches") (description @@ -16049,12 +15717,12 @@ interest.") ("guile" ,guile-3.0) ("guile-libyaml" ,guile-libyaml))) (native-inputs - `(("pkg-config" ,pkg-config) - ("lzip" ,lzip) - ;; To build documentation - ("cwltool" ,cwltool) - ("graphviz" ,graphviz) - ("skribilo" ,skribilo))) + (list pkg-config + lzip + ;; To build documentation + cwltool + graphviz + skribilo)) (home-page "https://ccwl.systemreboot.net") (synopsis "Concise common workflow language") (description "The @acronym{ccwl, Concise Common Workflow Language} is a |