diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 232 |
1 files changed, 116 insertions, 116 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7e97cdea7c..56837844b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -189,7 +189,7 @@ structure of the predicted RNA.") (method git-fetch) ;; BamM is not available on pypi. (uri (git-reference - (url "https://github.com/Ecogenomics/BamM.git") + (url "https://github.com/Ecogenomics/BamM") (commit version) (recursive? #t))) (file-name (git-file-name name version)) @@ -283,7 +283,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/pezmaster31/bamtools.git") + (url "https://github.com/pezmaster31/bamtools") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -361,7 +361,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/bedops/bedops.git") + (url "https://github.com/bedops/bedops") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -484,7 +484,7 @@ BED, GFF/GTF, VCF.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/PacificBiosciences/pbbam.git") + (url "https://github.com/PacificBiosciences/pbbam") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -540,7 +540,7 @@ Non-PacBio BAMs will cause exceptions to be thrown.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/PacificBiosciences/blasr_libcpp.git") + (url "https://github.com/PacificBiosciences/blasr_libcpp") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -602,7 +602,7 @@ hdf and alignment.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/PacificBiosciences/blasr.git") + (url "https://github.com/PacificBiosciences/blasr") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -693,7 +693,7 @@ provides the Ribotaper pipeline.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ratschlab/RiboDiff.git") + (url "https://github.com/ratschlab/RiboDiff") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -737,7 +737,7 @@ independently with transcriptional regulation.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/lh3/bioawk.git") + (url "https://github.com/lh3/bioawk") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -900,7 +900,7 @@ Python.") ;; Use GitHub as source because PyPI distribution does not contain ;; test data: https://github.com/biocore/biom-format/issues/693 (uri (git-reference - (url "https://github.com/biocore/biom-format.git") + (url "https://github.com/biocore/biom-format") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -1567,7 +1567,7 @@ errors at the end of reads.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/BenLangmead/bowtie2.git") + (url "https://github.com/BenLangmead/bowtie2") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -1783,7 +1783,7 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/pkerpedjiev/bwa-pssm.git") + (url "https://github.com/pkerpedjiev/bwa-pssm") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -1813,7 +1813,7 @@ well as many of the command line options.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/brentp/bwa-meth.git") + (url "https://github.com/brentp/bwa-meth") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -1887,7 +1887,7 @@ multiple sequence alignments.") (method git-fetch) ;; Test data is missing on PyPi. (uri (git-reference - (url "https://github.com/pysam-developers/pysam.git") + (url "https://github.com/pysam-developers/pysam") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -2036,7 +2036,7 @@ high-throughput sequencing data – with an emphasis on simplicity.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/mhammell-laboratory/tetoolkit.git") + (url "https://github.com/mhammell-laboratory/tetoolkit") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -2153,7 +2153,7 @@ databases.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/YeoLab/clipper.git") + (url "https://github.com/YeoLab/clipper") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -2412,7 +2412,7 @@ interval trees with associated meta-data. It is primarily used by the (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/deeptools/deepTools.git") + (url "https://github.com/deeptools/deepTools") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -2480,7 +2480,7 @@ other types of unwanted sequence from high-throughput sequencing reads.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dpryan79/libBigWig.git") + (url "https://github.com/dpryan79/libBigWig") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -2560,7 +2560,7 @@ accessing bigWig files.") (method git-fetch) ;; Source from GitHub so that tests are included. (uri (git-reference - (url "https://github.com/jeetsukumaran/DendroPy.git") + (url "https://github.com/jeetsukumaran/DendroPy") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -2618,7 +2618,7 @@ with Python.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dellytools/delly.git") + (url "https://github.com/dellytools/delly") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -2665,7 +2665,7 @@ accurately delineate genomic rearrangements throughout the genome.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/bbuchfink/diamond.git") + (url "https://github.com/bbuchfink/diamond") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -2700,7 +2700,7 @@ data and settings.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/maaskola/discrover.git") + (url "https://github.com/maaskola/discrover") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -2773,7 +2773,7 @@ of nucleic acid binding proteins.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/DReichLab/EIG.git") + (url "https://github.com/DReichLab/EIG") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -3021,7 +3021,7 @@ dynamic programming or a variety of heuristics.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/adarob/eXpress.git") + (url "https://github.com/adarob/eXpress") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -3072,7 +3072,7 @@ ChIP-Seq, and analysis of metagenomic data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dparks1134/ExpressBetaDiversity.git") + (url "https://github.com/dparks1134/ExpressBetaDiversity") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -3199,7 +3199,7 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/seqan/flexbar.git") + (url "https://github.com/seqan/flexbar") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -3342,7 +3342,7 @@ genes in incomplete assemblies or complete genomes.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ctSkennerton/fxtract.git") + (url "https://github.com/ctSkennerton/fxtract") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -3378,7 +3378,7 @@ genes in incomplete assemblies or complete genomes.") ,(origin (method git-fetch) (uri (git-reference - (url "https://github.com/ctSkennerton/util.git") + (url "https://github.com/ctSkennerton/util") (commit util-commit))) (file-name (string-append "ctstennerton-util-" util-commit "-checkout")) @@ -3405,7 +3405,7 @@ comment or quality sections.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/xiangzhou/GEMMA.git") + (url "https://github.com/xiangzhou/GEMMA") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -3465,7 +3465,7 @@ association studies (GWAS).") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/nboley/grit.git") + (url "https://github.com/nboley/grit") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -3690,7 +3690,7 @@ from high-throughput sequencing assays.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/samtools/htsjdk.git") + (url "https://github.com/samtools/htsjdk") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -3740,7 +3740,7 @@ manipulating HTS data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/samtools/htsjdk.git") + (url "https://github.com/samtools/htsjdk") (commit version))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -3784,7 +3784,7 @@ manipulating HTS data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/samtools/htsjdk.git") + (url "https://github.com/samtools/htsjdk") (commit version))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -3812,7 +3812,7 @@ manipulating HTS data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/broadinstitute/picard.git") + (url "https://github.com/broadinstitute/picard") (commit version))) (file-name (string-append "java-picard-" version "-checkout")) (sha256 @@ -3891,7 +3891,7 @@ VCF.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/broadinstitute/picard.git") + (url "https://github.com/broadinstitute/picard") (commit version))) (file-name (string-append "java-picard-" version "-checkout")) (sha256 @@ -3981,7 +3981,7 @@ VCF.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/broadinstitute/picard.git") + (url "https://github.com/broadinstitute/picard") (commit version))) (file-name (string-append "java-picard-" version "-checkout")) (sha256 @@ -4178,7 +4178,7 @@ The main functions of FastQC are: (origin (method git-fetch) (uri (git-reference - (url "https://github.com/OpenGene/fastp.git") + (url "https://github.com/OpenGene/fastp") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -4258,7 +4258,7 @@ data. It also provides the @command{bgzip}, @command{htsfile}, and (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/nboley/idr.git") + (url "https://github.com/nboley/idr") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -4349,7 +4349,7 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dib-lab/khmer.git") + (url "https://github.com/dib-lab/khmer") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -4457,7 +4457,7 @@ experiments.") ;; The PyPi tarball does not contain tests. (method git-fetch) (uri (git-reference - (url "https://github.com/taoliu/MACS.git") + (url "https://github.com/taoliu/MACS") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -4580,7 +4580,7 @@ sequences).") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/marbl/mash.git") + (url "https://github.com/marbl/mash") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -4719,7 +4719,7 @@ probabilistic distances of genome abundance and tetranucleotide frequency.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ctSkennerton/minced.git") + (url "https://github.com/ctSkennerton/minced") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -4861,7 +4861,7 @@ program for nucleotide and protein sequences.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/tjunier/newick_utils.git") + (url "https://github.com/tjunier/newick_utils") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -4999,7 +4999,7 @@ the phenotype as it models the data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/PacificBiosciences/cDNA_primer.git") + (url "https://github.com/PacificBiosciences/cDNA_primer") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -5220,7 +5220,7 @@ different command-line tools: (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/hyattpd/Prodigal.git") + (url "https://github.com/hyattpd/Prodigal") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -5369,7 +5369,7 @@ extremely diverse sets of genomes.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/stamatak/standard-RAxML.git") + (url "https://github.com/stamatak/standard-RAxML") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -5410,7 +5410,7 @@ phylogenies.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/deweylab/RSEM.git") + (url "https://github.com/deweylab/RSEM") (commit (string-append "v" version)))) (sha256 (base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1")) @@ -5699,7 +5699,7 @@ viewer.") ;; There are no release tarballs nor tags. (method git-fetch) (uri (git-reference - (url "https://github.com/wanpinglee/MOSAIK.git") + (url "https://github.com/wanpinglee/MOSAIK") (commit commit))) (file-name (string-append name "-" version)) (sha256 @@ -5745,7 +5745,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ncbi/ngs.git") + (url "https://github.com/ncbi/ngs") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -5811,7 +5811,7 @@ simultaneously.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ncbi/ncbi-vdb.git") + (url "https://github.com/ncbi/ncbi-vdb") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -5983,7 +5983,7 @@ subsequent visualization, annotation and storage of results.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/chrchang/plink-ng.git") + (url "https://github.com/chrchang/plink-ng") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -6022,7 +6022,7 @@ subsequent visualization, annotation and storage of results.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/smithlabcode/smithlab_cpp.git") + (url "https://github.com/smithlabcode/smithlab_cpp") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -6171,7 +6171,7 @@ sequence itself can be retrieved from these databases.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ncbi/sra-tools.git") + (url "https://github.com/ncbi/sra-tools") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -6381,7 +6381,7 @@ is one that takes arguments.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/lh3/seqtk.git") + (url "https://github.com/lh3/seqtk") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -6417,7 +6417,7 @@ optionally compressed by gzip.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/amplab/snap.git") + (url "https://github.com/amplab/snap") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -6459,7 +6459,7 @@ of these reads to align data quickly through a hash-based indexing scheme.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/biocore/sortmerna.git") + (url "https://github.com/biocore/sortmerna") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -6505,7 +6505,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/alexdobin/STAR.git") + (url "https://github.com/alexdobin/STAR") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -6733,7 +6733,7 @@ Cuffdiff or Ballgown programs.") ;; The Pypi version does not include tests. (method git-fetch) (uri (git-reference - (url "https://github.com/fhcrc/taxtastic.git") + (url "https://github.com/fhcrc/taxtastic") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -6858,7 +6858,7 @@ sequence.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/hms-dbmi/scde.git") + (url "https://github.com/hms-dbmi/scde") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -7304,7 +7304,7 @@ annotation infrastructure.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/torognes/vsearch.git") + (url "https://github.com/torognes/vsearch") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -8809,7 +8809,7 @@ in SNV base substitution data.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ManuSetty/ChIPKernels.git") + (url "https://github.com/ManuSetty/ChIPKernels") (commit commit))) (file-name (string-append name "-" version)) (sha256 @@ -8843,7 +8843,7 @@ Sequences.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ManuSetty/SeqGL.git") + (url "https://github.com/ManuSetty/SeqGL") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -9019,7 +9019,7 @@ tools for sequence analysis into a seamless whole.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/arq5x/bits.git") + (url "https://github.com/arq5x/bits") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -9065,7 +9065,7 @@ intervals (e.g. genes, sequence alignments).") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/smithlabcode/piranha.git") + (url "https://github.com/smithlabcode/piranha") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -9104,7 +9104,7 @@ intervals (e.g. genes, sequence alignments).") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/smithlabcode/smithlab_cpp.git") + (url "https://github.com/smithlabcode/smithlab_cpp") (commit commit))) (file-name (string-append "smithlab_cpp-" commit "-checkout")) (sha256 @@ -9157,7 +9157,7 @@ group or two ChIP groups run under different conditions.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ekg/filevercmp.git") + (url "https://github.com/ekg/filevercmp") (commit commit))) (file-name (git-file-name name commit)) (sha256 @@ -9234,7 +9234,7 @@ common bioinformatics tools.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/vatlab/varianttools.git") + (url "https://github.com/vatlab/varianttools") ;; There is no tag corresponding to version 3.1.2 (commit "813ae4a90d25b69abc8a40f4f70441fe09015249"))) (file-name (git-file-name name version)) @@ -11134,7 +11134,7 @@ Maximum Parsimony, distance methods and Hadamard conjugation.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/rajewsky-lab/dropbead.git") + (url "https://github.com/rajewsky-lab/dropbead") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -11164,7 +11164,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/lomereiter/htslib.git") + (url "https://github.com/lomereiter/htslib") (commit commit))) (file-name (string-append "htslib-" version "-checkout")) (sha256 @@ -11183,7 +11183,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/lomereiter/sambamba.git") + (url "https://github.com/lomereiter/sambamba") (commit (string-append "v" version)))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -11232,7 +11232,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/biod/BioD.git") + (url "https://github.com/biod/BioD") (commit commit))) (file-name (string-append "biod-" (string-take commit 9) @@ -11259,7 +11259,7 @@ sort, markdup, and depth.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/KlugerLab/Ritornello.git") + (url "https://github.com/KlugerLab/Ritornello") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -11305,7 +11305,7 @@ with narrow binding events such as transcription factor ChIP-seq.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/FelixKrueger/TrimGalore.git") + (url "https://github.com/FelixKrueger/TrimGalore") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -11520,7 +11520,7 @@ applications for tackling some common problems in a user-friendly way.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/3DGenomes/TADbit.git") + (url "https://github.com/3DGenomes/TADbit") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -11582,7 +11582,7 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ENCODE-DCC/kentUtils.git") + (url "https://github.com/ENCODE-DCC/kentUtils") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -11698,7 +11698,7 @@ browser.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/aboyle/F-seq.git") + (url "https://github.com/aboyle/F-seq") (commit commit))) (file-name (string-append name "-" version)) (sha256 @@ -11756,7 +11756,7 @@ Browser.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/FelixKrueger/Bismark.git") + (url "https://github.com/FelixKrueger/Bismark") (commit version))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -11908,7 +11908,7 @@ using nucleotide or amino-acid sequence data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/pachterlab/kallisto.git") + (url "https://github.com/pachterlab/kallisto") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -11957,7 +11957,7 @@ accurate as existing quantification tools.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/Kingsford-Group/libgff.git") + (url "https://github.com/Kingsford-Group/libgff") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -11980,7 +11980,7 @@ dependency like SeqAn.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/kingsfordgroup/sailfish.git") + (url "https://github.com/kingsfordgroup/sailfish") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -12095,7 +12095,7 @@ dependency like SeqAn.") ("rapmap" ,(origin (method git-fetch) (uri (git-reference - (url "https://github.com/COMBINE-lab/RapMap.git") + (url "https://github.com/COMBINE-lab/RapMap") (commit (string-append "sf-v" version)))) (file-name (string-append "rapmap-sf-v" version "-checkout")) (sha256 @@ -12130,7 +12130,7 @@ file(s) containing your reads.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/COMBINE-lab/staden-io_lib.git") + (url "https://github.com/COMBINE-lab/staden-io_lib") (commit (string-append "v" version)))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -12171,7 +12171,7 @@ The following file formats are supported: (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/COMBINE-lab/salmon.git") + (url "https://github.com/COMBINE-lab/salmon") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -12284,7 +12284,7 @@ The following file formats are supported: ("rapmap" ,(origin (method git-fetch) (uri (git-reference - (url "https://github.com/COMBINE-lab/RapMap.git") + (url "https://github.com/COMBINE-lab/RapMap") (commit (string-append "salmon-v" version)))) (file-name (string-append "rapmap-salmon-v" version "-checkout")) (sha256 @@ -12317,7 +12317,7 @@ variational inference.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/linnarsson-lab/loompy.git") + (url "https://github.com/linnarsson-lab/loompy") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -12360,7 +12360,7 @@ single-cell RNA-seq data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/cmzmasek/forester.git") + (url "https://github.com/cmzmasek/forester") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -13200,7 +13200,7 @@ HTML reports with interesting findings about your samples.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/jsh58/Genrich.git") + (url "https://github.com/jsh58/Genrich") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -13235,7 +13235,7 @@ enrichment.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/splatlab/mantis.git") + (url "https://github.com/splatlab/mantis") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -13302,7 +13302,7 @@ rate speciation and extinction.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/pervouchine/sjcount-full.git") + (url "https://github.com/pervouchine/sjcount-full") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 @@ -13447,7 +13447,7 @@ Thus the per-base error rate is similar to the raw input reads.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/BIMSBbioinfo/ciRcus.git") + (url "https://github.com/BIMSBbioinfo/ciRcus") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -13493,7 +13493,7 @@ can be calculated, and a number of descriptive plots easily generated.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/gpertea/gffread.git") + (url "https://github.com/gpertea/gffread") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -13527,7 +13527,7 @@ can be calculated, and a number of descriptive plots easily generated.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/gpertea/gclib.git") + (url "https://github.com/gpertea/gclib") (commit commit))) (file-name (git-file-name "gclib" version)) (sha256 @@ -13554,7 +13554,7 @@ conversions, region filtering, FASTA sequence extraction and more.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/marvin-jens/find_circ.git") + (url "https://github.com/marvin-jens/find_circ") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -13834,7 +13834,7 @@ bound.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/4dn-dcic/pairix.git") + (url "https://github.com/4dn-dcic/pairix") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -13933,7 +13933,7 @@ such as Hi-C contact matrices.") ;; Version 12 is not available on pypi. (method git-fetch) (uri (git-reference - (url "https://github.com/deeptools/HiCMatrix.git") + (url "https://github.com/deeptools/HiCMatrix") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -13973,7 +13973,7 @@ the HiCExplorer and pyGenomeTracks packages.") ;; The latest version is not available on Pypi. (method git-fetch) (uri (git-reference - (url "https://github.com/deeptools/HiCExplorer.git") + (url "https://github.com/deeptools/HiCExplorer") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -14122,7 +14122,7 @@ sequencing data.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/renozao/xbioc.git") + (url "https://github.com/renozao/xbioc") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -14155,7 +14155,7 @@ provided by Bioconductor packages.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/shenorrLab/csSAM.git") + (url "https://github.com/shenorrLab/csSAM") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -14186,7 +14186,7 @@ SAM.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/shenorrLab/bseqsc.git") + (url "https://github.com/shenorrLab/bseqsc") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -14234,7 +14234,7 @@ and intra-cell population structure.\" Baron et al. Cell Systems (2016) (origin (method git-fetch) (uri (git-reference - (url "https://github.com/rrwick/Porechop.git") + (url "https://github.com/rrwick/Porechop") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -14265,7 +14265,7 @@ Barcoding Kit or Rapid Barcoding Kit.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/arq5x/poretools.git") + (url "https://github.com/arq5x/poretools") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -14326,7 +14326,7 @@ absolute GSEA.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/mahmoudibrahim/JAMM.git") + (url "https://github.com/mahmoudibrahim/JAMM") (commit (string-append "JAMMv" version)))) (file-name (git-file-name name version)) (sha256 @@ -14526,7 +14526,7 @@ datasets.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/rrwick/Filtlong.git") + (url "https://github.com/rrwick/Filtlong") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -14587,7 +14587,7 @@ choosing which reads pass the filter.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/jts/nanopolish.git") + (url "https://github.com/jts/nanopolish") (commit commit) (recursive? #t))) (file-name (git-file-name name version)) @@ -14661,7 +14661,7 @@ polymorphisms) and indels with respect to a reference genome and more.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/etal/cnvkit.git") + (url "https://github.com/etal/cnvkit") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -14697,7 +14697,7 @@ Torrent.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/KlugerLab/pyFIt-SNE.git") + (url "https://github.com/KlugerLab/pyFIt-SNE") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -14960,7 +14960,7 @@ tools which build on STAR, Arriba does not require to reduce the (origin (method git-fetch) (uri (git-reference - (url "https://github.com/MikkelSchubert/adapterremoval.git") + (url "https://github.com/MikkelSchubert/adapterremoval") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -14999,7 +14999,7 @@ sequence for paired-ended data, for which this information is not available.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/matsen/pplacer.git") + (url "https://github.com/matsen/pplacer") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -15221,7 +15221,7 @@ on the needs of the user.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ParkerLab/ataqv.git") + (url "https://github.com/ParkerLab/ataqv") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -15262,7 +15262,7 @@ might be caused by ATAC-seq library prep or sequencing. The main program, (origin (method git-fetch) (uri (git-reference - (url "https://github.com/kcha/psiplot.git") + (url "https://github.com/kcha/psiplot") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -15293,7 +15293,7 @@ are generated using @code{ggplot2}.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/nanoporetech/ont_fast5_api.git") + (url "https://github.com/nanoporetech/ont_fast5_api") (commit (string-append "release_" version)))) (file-name (git-file-name name version)) (sha256 @@ -15324,7 +15324,7 @@ and reflect the fast5 file schema, and tools to convert between (origin (method git-fetch) (uri (git-reference - (url "https://github.com/phoenixding/tbsp.git") + (url "https://github.com/phoenixding/tbsp") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -15636,7 +15636,7 @@ manipulations on VCF files.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ekg/freebayes.git") + (url "https://github.com/ekg/freebayes") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -15754,7 +15754,7 @@ length of a short-read sequencing alignment.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/GregoryFaust/samblaster.git") + (url "https://github.com/GregoryFaust/samblaster") (commit (string-append "v." version)))) (file-name (git-file-name name version)) (sha256 @@ -15791,7 +15791,7 @@ pairs.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/velocyto-team/velocyto.R.git") + (url "https://github.com/velocyto-team/velocyto.R") (commit commit))) (file-name (git-file-name name version)) (sha256 @@ -15832,7 +15832,7 @@ patterns.") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/dpryan79/MethylDackel.git") + (url "https://github.com/dpryan79/MethylDackel") (commit version))) (file-name (git-file-name name version)) (sha256 @@ -15880,7 +15880,7 @@ containing the reference genome as well.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/daler/gffutils.git") + (url "https://github.com/daler/gffutils") (commit commit))) (file-name (git-file-name name version)) (sha256 |