diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 330 |
1 files changed, 160 insertions, 170 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 957c88d0c6..681919df3d 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 @@ -1327,15 +1327,15 @@ package provides command line tools using the Bio++ library.") (define-public blast+ (package (name "blast+") - (version "2.7.1") + (version "2.10.1") (source (origin (method url-fetch) (uri (string-append - "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/" + "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/" version "/ncbi-blast-" version "+-src.tar.gz")) (sha256 (base32 - "1jlq0afxxgczpp35k6mxh8mn4jzq7vqcnaixk166sfj10wq8v9qh")) + "11kvrrl0mcwww6530r55hccpg3x3msmhr3051fwnjbq8rzg2j1qi")) (modules '((guix build utils))) (snippet '(begin @@ -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 @@ -6986,14 +6986,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1inyxb89hd5bn0sl7a9qbv9d1g40z4v1s9qwxkcsx5c79fl04n1h")))) + "1m03awaw06mfv5gszq23k5apsqqzjqa5rcwp20y4xbpl7bywpsyl")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -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 @@ -7505,13 +7505,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.56.0") + (version "1.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1h4cmfbff79v9xrh271dp3rv0877ris06lmkvc39kqzj7yjsh7c2")))) + "0zcx8gha3x3jc0ra6ii6wwq2vfsmffrrnilknbq8h5xjrl55m6ci")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -7894,13 +7894,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.50.0") + (version "1.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "10gplxal0qphcn29azv0i6hiim9q45lmhzvhhhsnwfhwpgja7p05")))) + "00pd8lsdppxlmx0l65phw0jhsm0qkwjc4wsdxpvgc31iiz9yslbj")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -8092,13 +8092,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.18.1") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "07rc79k5dp0dnf4dvsxif995aa9cgfkf13yf84qnwl64k9pf3c2c")))) + "1raw5ycigr6gjgzn3kx3jls5hzww10fhnwd8c17c20hmhirf13rw")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -8205,13 +8205,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.40.0") + (version "1.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "09ffsflk2yhhj9ivm028y3qdkvv8idgxpm4il3y9rym7shc8b3f8")))) + "0zm7q957g952qyfqmvf27sldsnq6sqd0wlgnqzvmxayg9pxh0l0z")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -8415,7 +8415,7 @@ reference point and sorted by a user defined feature.") ("r-seqpattern" ,r-seqpattern))) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "http://bioinformatics.mdc-berlin.de/genomation/") + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Summary, annotation and visualization of genomic data") (description "This package provides a package for summary and annotation of genomic @@ -8448,7 +8448,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (arguments `(#:substitutable? #f)) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "http://bioinformatics.mdc-berlin.de/genomation/") + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Experimental data for use with the genomation package") (description "This package contains experimental genetic data for use with the @@ -8532,16 +8532,12 @@ two-dimensional genome scans.") (define-public r-qtl2 (package (name "r-qtl2") - (version "0.20") + (version "0.22-11") (source (origin - (method git-fetch) - ;; Not yet available in cran. - (uri (git-reference - (url "https://github.com/rqtl/qtl2.git") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0l1asr28q25jzbwrbg5490962sg3y4sjrd0qf09p78ws1aq8vfs0")))) + (method url-fetch) + (uri (cran-uri "qtl2" version)) + (sha256 + (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) @@ -8551,11 +8547,12 @@ two-dimensional genome scans.") ("r-rsqlite" ,r-rsqlite) ("r-yaml" ,r-yaml))) (home-page "https://kbroman.org/qtl2/") - (synopsis - "QTL analysis software for high-dimensional data and complex cross designs") + (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses") (description - "R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software -R/qtl, to better handle high-dimensional data and complex cross designs.") + "This package provides a set of tools to perform @dfn{Quantitative Trait +Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the +@code{R/qtl} package to better handle high-dimensional data and complex cross +designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.") (license license:gpl3))) (define-public r-zlibbioc @@ -8812,7 +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 @@ -8846,7 +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 @@ -8896,13 +8893,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.32.1") + (version "2.32.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "102zam2j43jwgaz9ch6y2jjbc3qf56ngmggikf99s8l3w9ggbskm")))) + "1v6ygi0avh3gmaj2ld2nr7vww4ipw39b5kqci9w27i3ja985lb8j")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) @@ -9022,7 +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 @@ -9068,7 +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 @@ -9107,7 +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 @@ -9160,7 +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 @@ -9237,7 +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)) @@ -10843,14 +10840,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "09ylwyk6a8sdrmi1mx7vpycpykqlqylmwa973g6jrcmk0h0qfa4w")) + "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9")) (modules '((guix build utils))) (snippet '(begin @@ -10870,14 +10867,7 @@ block processing.") (for-each delete-file '("configure" "configure.ac")) ;; Do not make other packages link with the proprietary libsz. (substitute* "R/zzz.R" - (("'\"%s/libhdf5.a\" \"%s/libsz.a\" -lz'") - "'\"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'") - (("'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libsz.a\" -lz'") - "'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'") - (("'%s/libhdf5_hl.a %s/libhdf5.a %s/libsz.a -lz'") - "'%s/libhdf5_hl.a %s/libhdf5.a %s/libhdf5.a -lz'") - (("'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'") - "'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'")) + ((" \"%s/libsz.a\"") "")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) @@ -10986,13 +10976,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.16.1") + (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0pi4mpc3lvskj5biyhc9cskcnz9q2wjmfrz7xdnx8qqd8vpy84g3")))) + "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -11066,14 +11056,14 @@ variable and significantly correlated genes.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "0i6gw8058gw9yajya3w9qq6l3p634fq9sv8dh8ifigxz0k9b98r6")))) + "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -11137,7 +11127,7 @@ 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 @@ -11167,7 +11157,7 @@ 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 @@ -11186,7 +11176,7 @@ 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 @@ -11235,7 +11225,7 @@ 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) @@ -11262,7 +11252,7 @@ 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 @@ -11308,7 +11298,7 @@ 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 @@ -11523,7 +11513,7 @@ 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 @@ -11585,7 +11575,7 @@ 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 @@ -11701,7 +11691,7 @@ 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 @@ -11759,7 +11749,7 @@ 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 @@ -11911,7 +11901,7 @@ 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 @@ -11960,7 +11950,7 @@ 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 @@ -11983,7 +11973,7 @@ 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 @@ -12098,7 +12088,7 @@ 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 @@ -12133,7 +12123,7 @@ 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 @@ -12174,7 +12164,7 @@ 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 @@ -12287,7 +12277,7 @@ 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 @@ -12320,7 +12310,7 @@ 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 @@ -12363,7 +12353,7 @@ 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 @@ -12569,7 +12559,7 @@ reading, writing, and exporting phylogenetic trees.") (native-inputs `(("java-junit" ,java-junit) ("java-hamcrest-core" ,java-hamcrest-core))) - (home-page "http://biojava.org") + (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 for processing biological data. It provides analytical and statistical @@ -12612,7 +12602,7 @@ This package provides the core libraries.") (native-inputs `(("java-junit" ,java-junit) ("java-hamcrest-core" ,java-hamcrest-core))) - (home-page "http://biojava.org") + (home-page "https://biojava.org") (synopsis "Biojava interface to the forester phylogenomics library") (description "The phylo module provides a biojava interface layer to the forester phylogenomics library for constructing phylogenetic trees."))) @@ -12649,7 +12639,7 @@ forester phylogenomics library for constructing phylogenetic trees."))) (native-inputs `(("java-junit" ,java-junit) ("java-hamcrest-core" ,java-hamcrest-core))) - (home-page "http://biojava.org") + (home-page "https://biojava.org") (synopsis "Biojava API for genetic sequence alignment") (description "The alignment module of BioJava provides an API that contains @@ -12706,7 +12696,7 @@ contains (native-inputs `(("java-junit" ,java-junit) ("java-hamcrest-core" ,java-hamcrest-core))) - (home-page "http://biojava.org") + (home-page "https://biojava.org") (synopsis "Biojava interface to the forester phylogenomics library") (description "The phylo module provides a biojava interface layer to the forester phylogenomics library for constructing phylogenetic trees."))) @@ -12743,7 +12733,7 @@ forester phylogenomics library for constructing phylogenetic trees."))) (native-inputs `(("java-junit" ,java-junit) ("java-hamcrest-core" ,java-hamcrest-core))) - (home-page "http://biojava.org") + (home-page "https://biojava.org") (synopsis "Biojava API for genetic sequence alignment") (description "The alignment module of BioJava provides an API that contains @@ -12955,7 +12945,7 @@ once. This package provides tools to perform Drop-seq analyses.") ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml))) - (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (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 reporting for RNA sequencing experiments. It is easy to use and produces high @@ -13024,7 +13014,7 @@ expression report comparing samples in an easily configurable manner.") ("kentutils" ,kentutils))) (native-inputs `(("python-pytest" ,python-pytest))) - (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (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 calling and reporting for ChIP sequencing experiments. It is easy to use and @@ -13086,7 +13076,7 @@ in an easily configurable manner.") ("trim-galore" ,trim-galore) ("cutadapt" ,cutadapt) ("samtools" ,samtools))) - (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (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 data of bisulfite experiments; it produces reports on aggregate methylation @@ -13150,7 +13140,7 @@ methylation and segmentation.") ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-stringr" ,r-stringr) ("r-yaml" ,r-yaml))) - (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") (description "PiGX scRNAseq is an analysis pipeline for preprocessing and quality control for single cell RNA sequencing experiments. The inputs are @@ -13179,7 +13169,7 @@ based methods.") ("pigx-chipseq" ,pigx-chipseq) ("pigx-rnaseq" ,pigx-rnaseq) ("pigx-scrnaseq" ,pigx-scrnaseq))) - (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipelines for genomics") (description "PiGx is a collection of genomics pipelines. It includes the following pipelines: @@ -13203,7 +13193,7 @@ 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 @@ -13238,7 +13228,7 @@ 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 @@ -13305,7 +13295,7 @@ 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 @@ -13450,7 +13440,7 @@ 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 @@ -13496,7 +13486,7 @@ 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 @@ -13530,7 +13520,7 @@ 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 @@ -13557,7 +13547,7 @@ 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 @@ -13837,7 +13827,7 @@ 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 @@ -13936,7 +13926,7 @@ 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 @@ -13976,7 +13966,7 @@ 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 @@ -14125,7 +14115,7 @@ 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 @@ -14158,7 +14148,7 @@ 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 @@ -14189,7 +14179,7 @@ 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 @@ -14237,7 +14227,7 @@ 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 @@ -14268,7 +14258,7 @@ 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 @@ -14329,7 +14319,7 @@ 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 @@ -14529,7 +14519,7 @@ 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 @@ -14590,7 +14580,7 @@ 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)) @@ -14664,7 +14654,7 @@ 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 @@ -14700,7 +14690,7 @@ 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 @@ -14963,7 +14953,7 @@ 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 @@ -15002,7 +14992,7 @@ 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 @@ -15224,7 +15214,7 @@ 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 @@ -15265,7 +15255,7 @@ 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 @@ -15296,7 +15286,7 @@ 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 @@ -15327,7 +15317,7 @@ 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 @@ -15639,7 +15629,7 @@ 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 @@ -15757,7 +15747,7 @@ 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 @@ -15794,7 +15784,7 @@ 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 @@ -15835,7 +15825,7 @@ 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 @@ -15883,7 +15873,7 @@ 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 |