(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))
(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
(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
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/PacificBiosciences/pbbam.git")
+ (url "https://github.com/PacificBiosciences/pbbam")
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(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/PacificBiosciences/blasr_libcpp.git")
+ (url "https://github.com/PacificBiosciences/blasr_libcpp")
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(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
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+ (url "https://github.com/PacificBiosciences/blasr")
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(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/ratschlab/RiboDiff.git")
+ (url "https://github.com/ratschlab/RiboDiff")
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(file-name (git-file-name name version))
(sha256
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/lh3/bioawk.git")
+ (url "https://github.com/lh3/bioawk")
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(file-name (git-file-name name version))
(sha256
;; 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")
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(file-name (git-file-name name version))
(sha256
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(method git-fetch)
(uri (git-reference
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(file-name (git-file-name name version))
(sha256
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(uri (git-reference
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(file-name (git-file-name name version))
(sha256
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(method git-fetch)
(uri (git-reference
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(file-name (git-file-name name version))
(sha256
(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")
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(file-name (git-file-name name version))
(sha256
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(uri (git-reference
- (url "https://github.com/mhammell-laboratory/tetoolkit.git")
+ (url "https://github.com/mhammell-laboratory/tetoolkit")
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(file-name (git-file-name name version))
(sha256
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(uri (git-reference
- (url "https://github.com/YeoLab/clipper.git")
+ (url "https://github.com/YeoLab/clipper")
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(file-name (git-file-name name version))
(sha256
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(uri (git-reference
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(file-name (git-file-name name version))
(sha256
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(uri (git-reference
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+ (url "https://github.com/dpryan79/libBigWig")
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(file-name (git-file-name name version))
(sha256
(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
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(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
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(uri (git-reference
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(file-name (git-file-name name version))
(sha256
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(file-name (git-file-name name version))
(sha256
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(file-name (git-file-name name version))
(sha256
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(file-name (git-file-name name version))
(sha256
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(file-name (git-file-name name version))
(sha256
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(uri (git-reference
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(file-name (git-file-name name version))
(sha256
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(uri (git-reference
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(file-name (git-file-name name version))
(sha256
,(origin
(method git-fetch)
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- (url "https://github.com/ctSkennerton/util.git")
+ (url "https://github.com/ctSkennerton/util")
(commit util-commit)))
(file-name (string-append
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(source (origin
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(uri (git-reference
- (url "https://github.com/xiangzhou/GEMMA.git")
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(file-name (git-file-name name version))
(sha256
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(method git-fetch)
(uri (git-reference
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(file-name (git-file-name name version))
(sha256
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(method git-fetch)
(uri (git-reference
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+ (url "https://github.com/samtools/htsjdk")
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(file-name (git-file-name name version))
(sha256
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(method git-fetch)
(uri (git-reference
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(file-name (string-append name "-" version "-checkout"))
(sha256
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- (url "https://github.com/samtools/htsjdk.git")
+ (url "https://github.com/samtools/htsjdk")
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(file-name (string-append name "-" version "-checkout"))
(sha256
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(uri (git-reference
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(file-name (string-append "java-picard-" version "-checkout"))
(sha256
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(file-name (string-append "java-picard-" version "-checkout"))
(sha256
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(file-name (string-append "java-picard-" version "-checkout"))
(sha256
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(file-name (git-file-name name version))
(sha256
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(file-name (git-file-name name version))
(sha256
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(uri (git-reference
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+ (url "https://github.com/dib-lab/khmer")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
;; 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
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(method git-fetch)
(uri (git-reference
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(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
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(method git-fetch)
(uri (git-reference
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(file-name (git-file-name name version))
(sha256
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(method git-fetch)
(uri (git-reference
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(file-name (string-append name "-" version "-checkout"))
(sha256
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(method git-fetch)
(uri (git-reference
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(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(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
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/stamatak/standard-RAxML.git")
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(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
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(uri (git-reference
- (url "https://github.com/deweylab/RSEM.git")
+ (url "https://github.com/deweylab/RSEM")
(commit (string-append "v" version))))
(sha256
(base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1"))
;; 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
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(uri (git-reference
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(file-name (git-file-name name version))
(sha256
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(method git-fetch)
(uri (git-reference
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(file-name (git-file-name name version))
(sha256
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/chrchang/plink-ng.git")
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(file-name (git-file-name name version))
(sha256
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(uri (git-reference
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(file-name (string-append name "-" version "-checkout"))
(sha256
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(method git-fetch)
(uri (git-reference
- (url "https://github.com/ncbi/sra-tools.git")
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(file-name (git-file-name name version))
(sha256
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(file-name (git-file-name name version))
(sha256
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(file-name (git-file-name name version))
(sha256
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(uri (git-reference
- (url "https://github.com/biocore/sortmerna.git")
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(file-name (git-file-name name version))
(sha256
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(uri (git-reference
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+ (url "https://github.com/alexdobin/STAR")
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(file-name (git-file-name name version))
(sha256
;; 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
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(file-name (git-file-name name version))
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(file-name (git-file-name name version))
(sha256
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(sha256
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(file-name (git-file-name name version))
(sha256
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(sha256
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(file-name (git-file-name name version))
(sha256
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(sha256
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(file-name (git-file-name name commit))
(sha256
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(uri (git-reference
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(file-name (git-file-name name version))
(origin
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(file-name (git-file-name name version))
(sha256
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(sha256
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(uri (git-reference
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(file-name (string-append name "-" version "-checkout"))
(sha256
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(file-name (string-append "biod-"
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(file-name (git-file-name name version))
(sha256
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(file-name (git-file-name name version))
(sha256
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(file-name (git-file-name name version))
(sha256
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(file-name (git-file-name name version))
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(sha256
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(file-name (git-file-name name version))
(sha256
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(file-name (git-file-name name version))
(sha256
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(file-name (git-file-name name version))
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(sha256
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(sha256
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(sha256
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(file-name (git-file-name name version))
(sha256
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(sha256
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(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
(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
(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
(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
(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
(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
(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
(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
;; 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
;; 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
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(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
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(method git-fetch)
(uri (git-reference
- (url "https://github.com/shenorrLab/csSAM.git")
+ (url "https://github.com/shenorrLab/csSAM")
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(file-name (git-file-name name version))
(sha256
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(method git-fetch)
(uri (git-reference
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+ (url "https://github.com/shenorrLab/bseqsc")
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(file-name (git-file-name name version))
(sha256
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(method git-fetch)
(uri (git-reference
- (url "https://github.com/rrwick/Porechop.git")
+ (url "https://github.com/rrwick/Porechop")
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(file-name (git-file-name name version))
(sha256
(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
(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
(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
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(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))
(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
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/KlugerLab/pyFIt-SNE.git")
+ (url "https://github.com/KlugerLab/pyFIt-SNE")
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(file-name (git-file-name name version))
(sha256
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(method git-fetch)
(uri (git-reference
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+ (url "https://github.com/MikkelSchubert/adapterremoval")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
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(method git-fetch)
(uri (git-reference
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+ (url "https://github.com/matsen/pplacer")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
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(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
(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
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(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
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(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
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(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
(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
(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
(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
(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