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2022-04-06gnu: Add r-rnaseqdtu.Hong Li
* gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-05gnu: pigx-scrnaseq: Set NUMBA_CACHE_DIR.Ricardo Wurmus
This is needed since the update of python-loompy. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Rename 'set-PYTHONPATH to 'set-additional-environment-variables and set NUMBA_CACHE_DIR.
2022-04-05gnu: pigx-scrnaseq: Use new inputs style.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.
2022-04-05gnu: pigx-scrnaseq: Update to 1.1.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.8. [patches]: Remove. [native-inputs]: Remove. * gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
2022-04-04gnu: freebayes: Fix test suite.Efraim Flashner
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python.
2022-04-04gnu: smithwaterman: Use new style for phases.Efraim Flashner
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list of G-Expressions.
2022-04-04gnu: smithwaterman: Fix cross-compiling.Efraim Flashner
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add make-flag to use cxx-for-target. Adjust custom 'patch-source and 'build-dynamic phases to use cross toolchain binaries when cross compiling. Remove trailing #t from phases.
2022-03-31gnu: python-velocyto: Set cache directory for Numba.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase 'set-numba-cache-dir.
2022-03-31gnu: wfmash: Enable test suite.Efraim Flashner
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable tests. Add custom 'check phase based on upstream's own CI tests. [native-inputs]: Add samtools.
2022-03-31gnu: Add wfmash.Arun Isaac
* gnu/packages/bioinformatics.scm (wfmash): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31gnu: htslib: Add bzip2 and xz to inputs.Arun Isaac
htslib links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz should be listed in inputs even though they are already present implicitly in native-inputs. Else, cross-compilation will fail. * gnu/packages/bioinformatics.scm (htslib)[inputs]: Add bzip2 and xz. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31gnu: python-loompy: Update to 3.0.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7. [arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir; respect TESTS? argument in 'check phase. [propagated-inputs]: Add python-click, python-numba, and python-numpy-groupies.
2022-03-29gnu: r-signac: Update to 1.6.0-2.458e647.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.6.0-2.458e647. [propagated-inputs]: Remove r-annotationfilter, r-biocgenerics, r-biostrings, r-biovizbase, and r-ggbio; add r-qlcmatrix and r-tidyselect. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-03-29gnu: plink-ng: Update to 2.00a3-20220315.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315.
2022-03-29gnu: Add r-cytobackbone.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-cytobackbone): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-03-29gnu: pigx-sars-cov2-ww: Update to 0.0.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5. [source]: Remove patch. [arguments]: Disable tests. * gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
2022-03-29gnu: pigx-rnaseq: Update to 0.0.20.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20. [source]: Remove patch. [inputs]: Add megadepth. * gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch. * gnu/local.mk (dist_patch_DATA): Remove it.
2022-03-09gnu: Add r-scopeloomr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scopeloomr): New variable.
2022-03-02gnu: texlive-latex-pgf: Rename to "texlive-pgf".Ludovic Courtès
Suggested by Ricardo Wurmus. * gnu/packages/tex.scm (texlive-latex-pgf): Rename to... (texlive-pgf): ... this. Change 'name' accordingly. (texlive-latex-pgf): Define as deprecated. (texlive-beamer)[propagated-inputs]: Use the new name. (texlive-todonotes)[propagated-inputs]: Likewise. (texlive-adjustbox)[propagated-inputs]: Likewise. (texlive-tcolorbox)[propagated-inputs]: Likewise. * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Likewise.
2022-02-27gnu: minimap2: Update to 2.24.Efraim Flashner
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.24.
2022-02-22gnu: Add r-dyngen.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dyngen): New variable.
2022-02-15gnu: python-gffutils: Update to 0.10.1.Marius Bakke
* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.10.1. [arguments]: Remove obsolete phase. Respect TESTS? in check phase while at it.
2022-01-31gnu: Add scvelo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scvelo): New variable.
2022-01-31gnu: python-louvain-0.6: Update to 0.7.1.Ricardo Wurmus
* gnu/packages/graph.scm (python-louvain-0.6): Update to 0.7.1. [arguments]: Add build phases 'find-igraph and 'pretend-version. [native-inputs]: Add python-setuptools-scm and python-wheel. Rename this variable... (python-louvain-0.7): ...to this, naturally. * gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Update reference to python-louvain-0.6.
2022-01-31gnu: bwa-meth: Remove trailing #T from build phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T from build phase.
2022-01-31gnu: bwa-meth: Update to 0.2.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3.
2022-01-27gnu: pigx-sars-cov2-ww: Fix Python module capture.Ricardo Wurmus
The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[arguments]: Set PYTHONPATH variable in new build phase.
2022-01-27gnu: pigx-scrnaseq: Fix Python module capture.Ricardo Wurmus
The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Set PYTHONPATH variable in new build phase.
2022-01-27gnu: pigx-bsseq: Fix Python module capture.Ricardo Wurmus
The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Set PYTHONPATH variable in new build phase.
2022-01-27gnu: pigx-chipseq: Fix Python module capture.Ricardo Wurmus
The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Set PYTHONPATH variable in new build phase.
2022-01-27gnu: pigx-rnaseq: Fix Python module capture.Ricardo Wurmus
The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Set PYTHONPATH variable in new build phase.
2022-01-22gnu: cwltool: Update to 3.1.20220119140128.Marius Bakke
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20220119140128. [propagated-inputs]: Change from PYTHON-RDFLIB-5 to PYTHON-RDFLIB. [native-inputs]: Remove PYTHON-RDFLIB-JSONLD.
2022-01-22gnu: python-pyvcf: Build with old setuptools.Marius Bakke
* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Add PYTHON-SETUPTOOLS.
2022-01-21gnu: Add r-scseqcomm.zimoun
* gnu/packages/bioinformatics.scm (r-scseqcomm): New variable.
2022-01-21gnu: Add r-icellnet.zimoun
* gnu/packages/bioinformatics.scm (r-icellnet): New variable.
2022-01-20gnu: samtools-0.1: Install headers and library.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add build phases 'install-library and 'install-headers.
2022-01-20gnu: Add r-doubletfinder.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-doubletfinder): New variable.
2022-01-18gnu: python-rdflib: Update to 6.1.1.Marius Bakke
* gnu/packages/rdf.scm (python-rdflib): Update to 6.1.1. [arguments]: Remove #:tests. Add #:phases. [native-inputs]: Change from PYTHON-NOSE to PYTHON-PYTEST. (python-rdflib-5): New variable. (python2-rdflib): Inherit from PYTHON-RDFLIB-5. * gnu/packages/python-xyz.scm (python-prov): Change from PYTHON-RDFLIB to PYTHON-RDFLIB-5. * gnu/packages/bioinformatics.scm (cwltool): Likewise.
2022-01-17Merge branch 'version-1.4.0'Maxim Cournoyer
With resolved conflicts in: gnu/packages/gnome.scm gnu/packages/openstack.scm gnu/packages/python-xyz.scm
2022-01-17gnu: sambamba: Update to 0.8.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.2. [arguments]: Sett CC and D_LD in build phase. [native-inputs]: Add ld-gold-wrapper and binutils-gold.
2022-01-10gnu: clipper: Remove obsolete phase.Sarah Morgensen
* gnu/packages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: python-biom-format: Remove obsolete phase.Sarah Morgensen
* gnu/packages/bioinformatics.scm (python-biom-format)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: python-pysam: Update to 0.18.0.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0. [source]: Add FIXME to clarify bundled libraries in use. [phases]{check}: Streamline. [propagated-inputs]: Use latest htslib (1.14). [native-inputs]: Use latest samtools and bcftools (1.14). Remove python-nose.
2022-01-10gnu: bcftools: Update to 1.14.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.14. (bcftools-1.12): New variable. (bcftools-1.10): Use package/inherit and delete trailing #t. [name]: Delete field.
2022-01-10gnu: samtools: Update to 1.14.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (samtools): Update to 1.14. [modules]: Delete argument. [phases]{install-library, install-headers}: Delete phases. This version no longer includes the legacy library (it links to htslib directly). (samtools-1.12): New variable.
2022-01-10gnu: htslib: Update to 1.14.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (htslib): Update to 1.14. (htslib-1.12): New variable. (htslib-1.10, htslib-1.9, htslib-1.3) (htslib-for-samtools-1.2): Normalize style.
2022-01-11gnu: stringtie: Update to 2.2.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (stringtie): Update to 2.2.0. [source]: Simplify snippet. [arguments]: Add make-flags; update build phases. [inputs]: Remove samtools-0.1; add bzip2, htslib-for-stringtie, and libdeflate. [license]: Change to Expat license.
2022-01-11gnu: Add htslib-for-stringtie.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib-for-stringtie): New variable. * gnu/packages/patches/htslib-for-stringtie.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2022-01-04gnu: r-archr: Update to 1.0.1-1.92ab814.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-archr): Update to 1.0.1-1.92ab814.
2021-12-30gnu: Remove trailing period from synopsis.Vagrant Cascadian
* gnu/packages/anddroid.scm (android-liblog, git-repo)[synopsis]: Remove trailing period. * gnu/packages/audio.scm (audio-to-midi)[synopsis]: Likewise. * gnu/packages/bioinformatics.scm (python-mygene, python-scanpy, nanosv)[synopsis]: Likewise. * gnu/packages/cran.scm (r-gsubfn)[synopsis]: Likewise. * gnu/packages/crates-io.scm (rust-ascii-1, rust-bindgen-0.59, rust-byte-unit-4, rust-clircle-0.3, rust-dashmap-4, rust-dhcp4r-0.2, rust-fast-float-0.2, rust-fst-0.4, rust-futures-core-preview-0.3, rust-http-types-2, rust-hyper-0.14, rust-indexmap-1, rust-minimal-lexical-0.1, rust-oorandom-11.1, rust-runtime-raw-0.3, rust-sharded-slab-0.1, rust-takeable-option-0.4, rust-tower-service-0.3, rust-ttf-parser-0.12)[synopsis]: Likewise. * gnu/packages/disk.scm (f3)[synopsis]: Likewise. * gnu/packages/emacs-xyz.scm (emacs-scribble-mode, emacs-psession)[synopsis]: Likewise. * gnu/packages/golang.scm (go-github-com-kylelemons-godebug)[synopsis]: Likewise. * gnu/packages/haskell-xyz.scm (ghc-fsnotify, ghc-libyaml, ghc-emojis, ghc-regex-tdfa, ghc-th-lift-instances, ghc-commonmark-pandoc)[synopsis]: Likewise. * gnu/packages/java.scm (java-commons-jxpath, java-jakarta-regexp)[synopsis]: Likewise. * gnu/packages/lisp-xyz.scm (sbcl-cl-annot, sbcl-envy)[synopsis]: Likewise. * gnu/packages/mail.scm (go-gitlab.com-shackra-goimapnotify)[synopsis]: Likewise. * gnu/packages/maven.scm (maven-wagon-http-shared, maven-surefire-plugin)[synopsis]: Likewise. * gnu/packages/perl.scm (perl-text-soundex)[synopsis]: Likewise. * gnu/packages/python-check.scm (python-httmock)[synopsis]: Likewise. * gnu/packages/python-web.scm (python-bottle)[synopsis]: Likewise. * gnu/packages/python-xyz.scm (python-olefile, python-tokenize-rt, python-pylzma)[synopsis]: Likewise. * gnu/packages/tex.scm (texlive-docstrip)[synopsis]: Likewise.
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