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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.
2020-12-29gnu: r-ggbio: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-ggbio): Move from here... * gnu/packages/bioconductor.scm (r-ggbio): ...to here.
2020-12-29gnu: r-gqtlstats: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here... * gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
2020-12-29gnu: r-snpstats: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-snpstats): Move from here... * gnu/packages/bioconductor.scm (r-snpstats): ...to here.
2020-12-29gnu: r-homo-sapiens: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here... * gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here. Replace 'string-append' by 'bioconductor-uri' with 'annotation'.
2020-12-29gnu: r-erma: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-erma): Move from here... * gnu/packages/bioconductor.scm (r-erma): ...to here.
2020-12-29gnu: r-ldblock: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-ldblock): Move from here... * gnu/packages/bioconductor.scm (r-ldblock): ...to here.
2020-12-29gnu: r-gqtlstats: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here... * gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
2020-12-29gnu: r-gviz: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-gviz): Move from here... * gnu/packages/bioconductor.scm (r-gviz): ...to here.
2020-12-29gnu: r-gwascat: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-gwascat): Move from here... * gnu/packages/bioconductor.scm (r-gwascat): ...to here.
2020-12-29gnu: r-sushi: Move to (gnu packages bioconductor).zimoun
* gnu/packages/bioinformatics.scm (r-sushi): Move from here... * gnu/packages/bioconductor.scm (r-sushi): ...to here.
2020-12-20gnu: kentutils: Build with OpenSSL 1.1.Marius Bakke
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL-1.0 to OPENSSL.
2020-12-20gnu: kentutils: Add a file name for the "samtabix" input.Marius Bakke
* gnu/packages/bioinformatics.scm (kentutils)[native-inputs]: For "samtabix", add a file name on the origin.
2020-12-09gnu: r-keggrest: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.1.
2020-12-09gnu: r-genomeinfodb: Update to 1.26.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.2.
2020-12-09gnu: r-biocstyle: Update to 2.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.1.
2020-12-09gnu: r-rhtslib: Propagate zlib.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib)[inputs]: Move zlib from here... [propagated-inputs]: ...to here. (r-variantannotation, r-rsamtools, r-bamsignals, r-rhdf5, r-methylkit)[inputs]: Remove zlib. * gnu/packages/bioconductor.scm (r-diffbind, r-quasr, r-cytolib, r-ncdfflow, r-flowworkspace, r-seqbias)[inputs]: Remove zlib.
2020-12-09gnu: r-gqtlstats: Update to 1.21.3.zimoun
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.21.3.
2020-12-09gnu: r-gqtlbase: Update to 1.21.1.zimoun
Co-authored-by: Ricardo Wurmus <rekado@elephly.net> * gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.21.1. [arguments]: Add phase to patch broken NAMESPACE file.
2020-12-09gnu: r-biocviews: Update to 1.58.1.zimoun
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.1. Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
2020-12-09gnu: r-rhdf5: Update to 2.34.0.zimoun
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.34.0. [propagated-inputs]: Add r-rhdf5filters. [arguments]: Avoid to have a plain directory on the list of libraries to link. Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
2020-12-09gnu: Add r-rhdf5filters.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable.
2020-12-09gnu: r-genomationdata: Update to 1.22.0.zimoun
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.22.0.
2020-12-09gnu: r-sushi: Update to 1.28.0.zimoun
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.28.0.
2020-12-09gnu: r-gwascat: Update to 2.22.0.zimoun
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.22.0. [propagated-inputs]: Add r-biocfilecache, r-readr, r-snpstats, and r-variantannotation; remove r-biocgenerics, r-ggplot2, r-rsamtools, and r-rtracklayer.
2020-12-09gnu: r-gviz: Update to 1.34.0.zimoun
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.34.0.
2020-12-09gnu: r-ldblock: Update to 1.20.0.zimoun
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.20.0.
2020-12-09gnu: r-erma: Update to 1.6.0.zimoun
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.6.0.
2020-12-09gnu: r-snpstats: Update to 1.40.0.zimoun
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.40.0.
2020-12-09gnu: r-ggbio: Update to 1.38.0.zimoun
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.38.0.
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