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2021-03-06gnu: seqan-1: Use HTTPS source URI.Nicolas Goaziou
* gnu/packages/bioinformatics.scm (seqan-1)[source]: Use HTTPS URI.
2021-03-06gnu: seqan: Use HTTPS home page URI.Nicolas Goaziou
* gnu/packages/bioinformatics.scm (seqan)[home-page]: Use HTTPS URI.
2021-03-05gnu: Add r-cellchat.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-cellchat): New variable.
2021-03-03gnu: infernal: Update to 1.1.4.Tim Howes
* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.4. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-03-03gnu: hmmer: Update to 3.3.2.Tim Howes
* gnu/packages/bioinformatics.scm (hmmer): Update to 3.3.2. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-03-02gnu: kallisto: Update to 0.46.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.46.2. [source]: Remove bundled htslib sources.
2021-03-02gnu: kallisto: Use older htslib.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kallisto)[inputs]: Use htslib-1.9 instead of the latest.
2021-02-28gnu: f-seq: Use HTTPS home page URI.Nicolas Goaziou
* gnu/packages/bioinformatics.scm (f-seq)[home-page]: Use HTTPS URI.
2021-02-23gnu: Add star-for-pigx.Ricardo Wurmus
This is a follow-up to commit f1f6e49190a11f926af3bef0d45541cabf47c742. * gnu/packages/bioinformatics.scm (star-for-pigx): New variable. (pigx-rnaseq, pigx-scrnaseq)[inputs]: Replace star with star-for-pigx.
2021-02-22gnu: star: Update to 2.7.8a.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (star): Update to 2.7.8a.
2021-02-19gnu: nanopolish: Fix script wrapping.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (nanopolish)[arguments]: Fix wrap-programs phase. [inputs]: Add Guile for wrap-script; add bioperl and perl-getopt-long for Perl scripts.
2021-02-19gnu: Add prinseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (prinseq): New variable.
2021-02-19gnu: Add ngshmmalign.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngshmmalign): New variable.
2021-02-18gnu: Add r-archr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-archr): New variable.
2021-02-15gnu: Add indelfixer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (indelfixer): New variable.
2021-02-11gnu: bowtie1: Update to 1.3.0.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.3.0. [arguments]: Set CC in make flags. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-02-11gnu: r-gage: Update to 2.40.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.1.
2021-02-11gnu: r-msnbase: Update to 2.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.1.
2021-02-11gnu: r-methylkit: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.1.
2021-02-11gnu: r-delayedarray: Update to 0.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.1.
2021-02-11gnu: r-biomart: Update to 2.46.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.3.
2021-02-11gnu: r-edger: Update to 3.32.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.1.
2021-02-11gnu: r-iranges: Update to 2.24.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.1.
2021-02-11gnu: r-s4vectors: Update to 0.28.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.1.
2021-02-11gnu: r-systempiper: Update to 1.24.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.3.
2021-02-11gnu: r-gseabase: Update to 1.52.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.1.
2021-02-11gnu: r-genefilter: Update to 1.72.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.1.
2021-02-05gnu: rsem: Link with shared libhts library.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Link with libhts.so instead of libhts.a.
2021-02-01gnu: vcflib: Fix generated pkg-config file.Efraim Flashner
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In custom generated pkg-config file, link with all needed libraries and fix linker library. * gnu/packages/patches/freebayes-devendor-deps.patch: Adjust accordingly.
2021-01-29gnu: grocsvs: Remove package.Maxim Cournoyer
This package depends on Python 2 and doesn't build anymore. Upstream doesn't seem active, but if they ever port it to Python 3, they should let people know here: https://github.com/grocsvs/grocsvs/issues/6. * gnu/packages/bioinformatics.scm (grocsvs): Delete.
2021-01-28gnu: Add r-demultiplex.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-demultiplex): New variable.
2021-01-28gnu: Add repeat-masker.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (repeat-masker): New variable.
2021-01-28gnu: Add trf.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (trf): New variable.
2021-01-19gnu: freebayes: Update source, home-page URIs.Efraim Flashner
* gnu/packages/bioinformatics.scm (freebayes)[source]: Update to new upstream URI. [home-page]: Same.
2021-01-19gnu: freebayes: Don't include vcflib sources.Efraim Flashner
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Remove vcflib-source, intervaltree-source. Move vcflib ... [inputs]: ... to here. [arguments]: Adjust 'patch-source and 'unpack-submodule-sources for changes in vendored code. * gnu/packages/patches/freebayes-devendor-deps.patch: Update patch.
2021-01-19gnu: vcflib: Add pkg-config file.Efraim Flashner
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to create pkg-config file.
2021-01-19gnu: vcflib: Build a shared library.Efraim Flashner
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to build a shared library instead of a static one.
2021-01-19gnu: freebayes: Extend test timeout on slower architectures.Efraim Flashner
* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Use custom 'check phase on aarch64-linux and armhf-linux to extend the test timeout.
2021-01-18gnu: Add r-snapatac.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-snapatac): New variable.
2021-01-18gnu: mafft: Update to 7.475.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (mafft): Update to 7.475. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-01-18gnu: ruby-bio-vcf: Rename to bio-vcf.Efraim Flashner
This package is widely known in select circles specifically as 'bio-vcf'. * gnu/packages/bioinformatics.scm (ruby-bio-vcf): Rename to bio-vcf.
2021-01-18gnu: Add ruby-bio-vcf.Efraim Flashner
* gnu/packages/bioinformatics.scm (ruby-bio-vcf): New variable.
2021-01-17gnu: freebayes: Update to 1.3.3.Efraim Flashner
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.3. [source]: Add patch. Add snippet to remove vendored library. [build-system]: Switch to meson-build-system. [inputs]: Remove bamtools. Add fastahack, smithwaterman, tabixpp. [native-inputs]: Remove procps, python-2, tabixpp source, smithwaterman source, multichoose source, fsom source, filevercmp source, fastahack source, bash-tap source. Add bash-tap, grep, pkg-config, simde, vcflib. [arguments]: Drop make-flags. Don't delete 'configure phase. Delete custom 'fix-tests, 'build-tabixpp-and-vcflib, 'fix-makefiles, 'install phases. Adjust 'unpack-submodule-sources phase to changed native-inputs. Add new 'patch-source phase.
2021-01-17gnu: multichoose: Install header files.Efraim Flashner
* gnu/packages/bioinformatics.scm (multichoose)[arguments]: Adjust 'install phase to also install header files.
2021-01-17gnu: filevercmp: Install header files.Efraim Flashner
* gnu/packages/bioinformatics.scm (filevercmp)[arguments]: Adjust 'install phase to install header files.
2021-01-14gnu: vcflib: Update to 1.0.2.Efraim Flashner
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.2. [source]: Download using git-fetch. Remove patch. Update snippet to use packaged libraries. [build-system]: Switch to cmake-build-system. [inputs]: Add bzip2. [native-inputs]: Add package-source of fsom. [arguments]: Delete custom 'set-flags, 'install phases. Don't delete 'configure phase. Adjust 'unpack-submodule-sources phase. * gnu/packages/patches/vcflib-use-shared-libraries.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
2021-01-14gnu: sambamba Update to 0.8.0.Efraim Flashner
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.0. [source, home-page]: Update to new upstream URI. [arguments]: Shorten 'fix-ldc-version phase. Remove 'place-biod-and-undead phase. Update 'unbundle-prerequisites and 'insatll phases. [native-inputs]: Remove rdmd, biod. Move ldc ... [inputs]: ... to here. Add zlib. (htslib-for-sambamba): Remove variable.
2021-01-14gnu: gemma: Enable tests.Efraim Flashner
* gnu/packages/bioinformatics.scm (gemma)[source]: Add snippet to remove bundled sources. [native-inputs]: Add catch-framework2-1, perl, shunit2, which. [arguments]: Don't disable tests. Override 'check phase.
2021-01-14gnu: gemma: Add Texinfo markup.Efraim Flashner
* gnu/packages/bioinformatics.scm (gemma)[description]: Use Texinfo markup.
2021-01-14gnu: gemma: Update to 0.98.3.Efraim Flashner
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.3. [source, home-page]: Update to new upstream URI. [inputs]: Remove eigen, gfortran, lapack. [arguments]: Remove make-flags. Remove 'find-eigen phase. Rename 'bin-mkdir phase to 'prepare-build and substitute openblas include directory.
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