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gnu: Remove ".git" from "https://github/…/….git".

Browse source 
Until now, 'lookup-origin' and thus 'lookup-origin-revision' in (guix
swh) would sometimes return #f for these because the ".git" URLs are
redirects to the non-".git" URLs.  Consequently, 'guix lint -c archival'
would keep saying "scheduled Software Heritage archival"; likewise, the
fallback download code would fail.

* gnu/packages/ada.scm,
gnu/packages/admin.scm,
gnu/packages/aidc.scm,
gnu/packages/algebra.scm,
gnu/packages/android.scm,
gnu/packages/animation.scm,
gnu/packages/arcan.scm,
gnu/packages/assembly.scm,
gnu/packages/audio.scm,
gnu/packages/authentication.scm,
gnu/packages/avr.scm,
gnu/packages/axoloti.scm,
gnu/packages/backup.scm,
gnu/packages/bash.scm,
gnu/packages/benchmark.scm,
gnu/packages/bioconductor.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/bittorrent.scm,
gnu/packages/boost.scm,
gnu/packages/build-tools.scm,
gnu/packages/c.scm,
gnu/packages/calendar.scm,
gnu/packages/cdrom.scm,
gnu/packages/check.scm,
gnu/packages/chemistry.scm,
gnu/packages/chez.scm,
gnu/packages/clojure.scm,
gnu/packages/code.scm,
gnu/packages/compression.scm,
gnu/packages/compton.scm,
gnu/packages/coq.scm,
gnu/packages/cpp.scm,
gnu/packages/cran.scm,
gnu/packages/crypto.scm,
gnu/packages/curl.scm,
gnu/packages/databases.scm,
gnu/packages/datastructures.scm,
gnu/packages/debug.scm,
gnu/packages/disk.scm,
gnu/packages/distributed.scm,
gnu/packages/django.scm,
gnu/packages/dlang.scm,
gnu/packages/dns.scm,
gnu/packages/docker.scm,
gnu/packages/education.scm,
gnu/packages/efi.scm,
gnu/packages/elixir.scm,
gnu/packages/emacs-xyz.scm,
gnu/packages/embedded.scm,
gnu/packages/emulators.scm,
gnu/packages/engineering.scm,
gnu/packages/erlang.scm,
gnu/packages/fabric-management.scm,
gnu/packages/file-systems.scm,
gnu/packages/finance.scm,
gnu/packages/firmware.scm,
gnu/packages/flashing-tools.scm,
gnu/packages/fonts.scm,
gnu/packages/fontutils.scm,
gnu/packages/fpga.scm,
gnu/packages/game-development.scm,
gnu/packages/games.scm,
gnu/packages/genealogy.scm,
gnu/packages/genimage.scm,
gnu/packages/geo.scm,
gnu/packages/gimp.scm,
gnu/packages/gl.scm,
gnu/packages/gnome-xyz.scm,
gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm,
gnu/packages/golang.scm,
gnu/packages/gpodder.scm,
gnu/packages/graph.scm,
gnu/packages/graphics.scm,
gnu/packages/graphviz.scm,
gnu/packages/groff.scm,
gnu/packages/groovy.scm,
gnu/packages/gtk.scm,
gnu/packages/guile-xyz.scm,
gnu/packages/guile.scm,
gnu/packages/hardware.scm,
gnu/packages/haskell-apps.scm,
gnu/packages/haskell-xyz.scm,
gnu/packages/hexedit.scm,
gnu/packages/i2p.scm,
gnu/packages/ibus.scm,
gnu/packages/image-processing.scm,
gnu/packages/image-viewers.scm,
gnu/packages/image.scm,
gnu/packages/ipfs.scm,
gnu/packages/java-graphics.scm,
gnu/packages/java-maths.scm,
gnu/packages/java.scm,
gnu/packages/javascript.scm,
gnu/packages/jrnl.scm,
gnu/packages/julia.scm,
gnu/packages/jupyter.scm,
gnu/packages/kodi.scm,
gnu/packages/language.scm,
gnu/packages/lego.scm,
gnu/packages/less.scm,
gnu/packages/libusb.scm,
gnu/packages/linux.scm,
gnu/packages/lirc.scm,
gnu/packages/lisp-xyz.scm,
gnu/packages/llvm.scm,
gnu/packages/logging.scm,
gnu/packages/lolcode.scm,
gnu/packages/lua.scm,
gnu/packages/lxde.scm,
gnu/packages/lxqt.scm,
gnu/packages/machine-learning.scm,
gnu/packages/mail.scm,
gnu/packages/markup.scm,
gnu/packages/maths.scm,
gnu/packages/maven.scm,
gnu/packages/mes.scm,
gnu/packages/messaging.scm,
gnu/packages/monitoring.scm,
gnu/packages/mpd.scm,
gnu/packages/music.scm,
gnu/packages/networking.scm,
gnu/packages/node-xyz.scm,
gnu/packages/ocaml.scm,
gnu/packages/ocr.scm,
gnu/packages/onc-rpc.scm,
gnu/packages/opencl.scm,
gnu/packages/opencog.scm,
gnu/packages/pantheon.scm,
gnu/packages/password-utils.scm,
gnu/packages/patchutils.scm,
gnu/packages/pdf.scm,
gnu/packages/perl6.scm,
gnu/packages/phabricator.scm,
gnu/packages/popt.scm,
gnu/packages/printers.scm,
gnu/packages/prolog.scm,
gnu/packages/protobuf.scm,
gnu/packages/pulseaudio.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/python-xyz.scm,
gnu/packages/qt.scm,
gnu/packages/radio.scm,
gnu/packages/rails.scm,
gnu/packages/rdf.scm,
gnu/packages/rednotebook.scm,
gnu/packages/rpc.scm,
gnu/packages/rsync.scm,
gnu/packages/ruby.scm,
gnu/packages/rust.scm,
gnu/packages/scheme.scm,
gnu/packages/screen.scm,
gnu/packages/security-token.scm,
gnu/packages/selinux.scm,
gnu/packages/serialization.scm,
gnu/packages/shells.scm,
gnu/packages/shellutils.scm,
gnu/packages/simh.scm,
gnu/packages/sml.scm,
gnu/packages/ssh.scm,
gnu/packages/statistics.scm,
gnu/packages/stenography.scm,
gnu/packages/sync.scm,
gnu/packages/syncthing.scm,
gnu/packages/synergy.scm,
gnu/packages/telephony.scm,
gnu/packages/terminals.scm,
gnu/packages/tex.scm,
gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm,
gnu/packages/textutils.scm,
gnu/packages/time.scm,
gnu/packages/tmux.scm,
gnu/packages/tor.scm,
gnu/packages/toys.scm,
gnu/packages/version-control.scm,
gnu/packages/video.scm,
gnu/packages/vim.scm,
gnu/packages/virtualization.scm,
gnu/packages/vlang.scm,
gnu/packages/vnc.scm,
gnu/packages/vpn.scm,
gnu/packages/web-browsers.scm,
gnu/packages/web.scm,
gnu/packages/wireservice.scm,
gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm,
gnu/packages/xdisorg.scm,
gnu/packages/xml.scm,
gnu/packages/xorg.scm,
tests/lint.scm: Remove trailing ".git" from 'git-reference' URL.
This commit is contained in:
Ludovic Courtès 2020-07-12 22:53:28 +02:00
parent c10526672e
commit b0e7b6992f
No known key found for this signature in database
GPG key ID: 090B11993D9AEBB5
192 changed files with 1673 additions and 1673 deletions
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232
gnu/packages/bioinformatics.scm
View file

@ -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
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(url "https://github.com/ncbi/ncbi-vdb.git")
(url "https://github.com/ncbi/ncbi-vdb")
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@ -5983,7 +5983,7 @@ subsequent visualization, annotation and storage of results.")
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@ -6022,7 +6022,7 @@ subsequent visualization, annotation and storage of results.")
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(url "https://github.com/smithlabcode/smithlab_cpp")
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@ -6171,7 +6171,7 @@ sequence itself can be retrieved from these databases.")
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(url "https://github.com/ncbi/sra-tools")
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@ -6381,7 +6381,7 @@ is one that takes arguments.")
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(url "https://github.com/lh3/seqtk.git")
(url "https://github.com/lh3/seqtk")
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@ -6417,7 +6417,7 @@ optionally compressed by gzip.")
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(url "https://github.com/amplab/snap.git")
(url "https://github.com/amplab/snap")
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@ -6459,7 +6459,7 @@ of these reads to align data quickly through a hash-based indexing scheme.")
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(url "https://github.com/biocore/sortmerna.git")
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@ -6505,7 +6505,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
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(url "https://github.com/alexdobin/STAR.git")
(url "https://github.com/alexdobin/STAR")
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@ -6733,7 +6733,7 @@ Cuffdiff or Ballgown programs.")
;; The Pypi version does not include tests.
(method git-fetch)
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(url "https://github.com/fhcrc/taxtastic.git")
(url "https://github.com/fhcrc/taxtastic")
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@ -6858,7 +6858,7 @@ sequence.")
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@ -7304,7 +7304,7 @@ annotation infrastructure.")
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@ -8809,7 +8809,7 @@ in SNV base substitution data.")
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@ -8843,7 +8843,7 @@ Sequences.")
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@ -9019,7 +9019,7 @@ tools for sequence analysis into a seamless whole.")
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(url "https://github.com/arq5x/bits")
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@ -9065,7 +9065,7 @@ intervals (e.g. genes, sequence alignments).")
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@ -9104,7 +9104,7 @@ intervals (e.g. genes, sequence alignments).")
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@ -9157,7 +9157,7 @@ group or two ChIP groups run under different conditions.")
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(url "https://github.com/ekg/filevercmp")
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@ -9234,7 +9234,7 @@ common bioinformatics tools.")
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(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")))
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@ -11134,7 +11134,7 @@ Maximum Parsimony, distance methods and Hadamard conjugation.")
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@ -11164,7 +11164,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
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@ -11183,7 +11183,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
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@ -11232,7 +11232,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.")
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@ -11259,7 +11259,7 @@ sort, markdup, and depth.")
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@ -11305,7 +11305,7 @@ with narrow binding events such as transcription factor ChIP-seq.")
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@ -11520,7 +11520,7 @@ applications for tackling some common problems in a user-friendly way.")
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@ -11582,7 +11582,7 @@ models. TADbit is complemented by TADkit for visualizing 3D models.")
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@ -11698,7 +11698,7 @@ browser.")
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@ -11756,7 +11756,7 @@ Browser.")
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@ -11908,7 +11908,7 @@ using nucleotide or amino-acid sequence data.")
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@ -11957,7 +11957,7 @@ accurate as existing quantification tools.")
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@ -11980,7 +11980,7 @@ dependency like SeqAn.")
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@ -12095,7 +12095,7 @@ dependency like SeqAn.")
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@ -12130,7 +12130,7 @@ file(s) containing your reads.")
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@ -12171,7 +12171,7 @@ The following file formats are supported:
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@ -12284,7 +12284,7 @@ The following file formats are supported:
("rapmap" ,(origin
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(uri (git-reference
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(url "https://github.com/COMBINE-lab/RapMap")
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@ -12317,7 +12317,7 @@ variational inference.")
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(url "https://github.com/linnarsson-lab/loompy")
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@ -12360,7 +12360,7 @@ single-cell RNA-seq data.")
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(url "https://github.com/cmzmasek/forester")
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@ -13200,7 +13200,7 @@ HTML reports with interesting findings about your samples.")
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(url "https://github.com/jsh58/Genrich")
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@ -13235,7 +13235,7 @@ enrichment.")
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(url "https://github.com/splatlab/mantis")
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@ -13302,7 +13302,7 @@ rate speciation and extinction.")
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(url "https://github.com/pervouchine/sjcount-full")
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@ -13447,7 +13447,7 @@ Thus the per-base error rate is similar to the raw input reads.")
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(url "https://github.com/BIMSBbioinfo/ciRcus.git")
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@ -13493,7 +13493,7 @@ can be calculated, and a number of descriptive plots easily generated.")
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@ -13527,7 +13527,7 @@ can be calculated, and a number of descriptive plots easily generated.")
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@ -13554,7 +13554,7 @@ conversions, region filtering, FASTA sequence extraction and more.")
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@ -13834,7 +13834,7 @@ bound.")
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(url "https://github.com/4dn-dcic/pairix")
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@ -13933,7 +13933,7 @@ such as Hi-C contact matrices.")
;; Version 12 is not available on pypi.
(method git-fetch)
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(url "https://github.com/deeptools/HiCMatrix.git")
(url "https://github.com/deeptools/HiCMatrix")
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@ -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")
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@ -14122,7 +14122,7 @@ sequencing data.")
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@ -14155,7 +14155,7 @@ provided by Bioconductor packages.")
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(url "https://github.com/shenorrLab/csSAM")
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@ -14186,7 +14186,7 @@ SAM.")
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@ -14234,7 +14234,7 @@ and intra-cell population structure.\" Baron et al. Cell Systems (2016)
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@ -14265,7 +14265,7 @@ Barcoding Kit or Rapid Barcoding Kit.")
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@ -14326,7 +14326,7 @@ absolute GSEA.")
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@ -14526,7 +14526,7 @@ datasets.")
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@ -14587,7 +14587,7 @@ choosing which reads pass the filter.")
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(url "https://github.com/jts/nanopolish")
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@ -14661,7 +14661,7 @@ polymorphisms) and indels with respect to a reference genome and more.")
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(url "https://github.com/etal/cnvkit")
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@ -14697,7 +14697,7 @@ Torrent.")
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(url "https://github.com/KlugerLab/pyFIt-SNE")
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@ -14960,7 +14960,7 @@ tools which build on STAR, Arriba does not require to reduce the
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@ -14999,7 +14999,7 @@ sequence for paired-ended data, for which this information is not available.")
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(url "https://github.com/matsen/pplacer")
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@ -15221,7 +15221,7 @@ on the needs of the user.")
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(url "https://github.com/ParkerLab/ataqv.git")
(url "https://github.com/ParkerLab/ataqv")
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@ -15262,7 +15262,7 @@ might be caused by ATAC-seq library prep or sequencing. The main program,
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(url "https://github.com/kcha/psiplot")
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@ -15293,7 +15293,7 @@ are generated using @code{ggplot2}.")
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@ -15324,7 +15324,7 @@ and reflect the fast5 file schema, and tools to convert between
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@ -15636,7 +15636,7 @@ manipulations on VCF files.")
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@ -15754,7 +15754,7 @@ length of a short-read sequencing alignment.")
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@ -15791,7 +15791,7 @@ pairs.")
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(url "https://github.com/velocyto-team/velocyto.R")
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@ -15832,7 +15832,7 @@ patterns.")
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(url "https://github.com/dpryan79/MethylDackel.git")
(url "https://github.com/dpryan79/MethylDackel")
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@ -15880,7 +15880,7 @@ containing the reference genome as well.")
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