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2023-05-05Revert "gnu: Add python-gimmemotifs."Ricardo Wurmus
This reverts commit dc8b3ebe5d4ba2a39c12f62d836963ffee1e4b47. python-gimmemotifs is not usable without proprietary third-party tools.
2023-05-05gnu: Add python-gimmemotifs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-gimmemotifs): New variable.
2023-05-05gnu: Add python-biofluff.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biofluff): New variable.
2023-05-05gnu: Add python-genomepy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-genomepy): New variable.
2023-05-05gnu: Add python-logomaker.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-logomaker): New variable.
2023-05-05gnu: python-pyfaidx: Update to 0.7.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.7.2.1. [build-system]: Use pyproject-build-system. [arguments]: Ignore tests that require large downloads. [native-inputs]: Remove python-six; add python-fsspec, python-pytest, python-pytest-cov, python-mock, and python-numpy.
2023-05-04gnu: python-screed: Update to 1.1.2.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-screed): Update to 1.1.2. [build-system]: Use pyproject-build-system. [native-inputs]: Remove python-pytest. [inputs]: Remove python-bz2file. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-05-04gnu: Add python-goatools.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-goatools): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-05-03gnu: pigx-sars-cov-2: Update to 0.0.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.9.
2023-05-03gnu: Add fanc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fanc): New variable.
2023-04-29gnu: r-tictoc: Update to 1.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-tictoc): Update to 1.2.
2023-04-27gnu: gdcm: Disable dependent tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Disable tests that depend on the output of a disabled test.
2023-04-27gnu: freebayes: Update to 1.3.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.7. [arguments]: Do not use "grep -P" in tests; drop trailing #T.
2023-04-27gnu: vcflib: Use libwfa2.pc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vcflib)[source]: Use pkg-config to look for libwfa2. [inputs]: Move wfa2-lib from here... [propagated-inputs]: ...to here. [arguments]: Drop WFA_LINK_LIBRARIES option; fix typo in build phase name; patch IntervalTree.h includes; add libwfa2 to pkg-config file.
2023-04-27gnu: wfa2-lib: Install pkg-config file.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (wfa2-lib)[arguments]: Install libwfa2.pc.
2023-04-27gnu: express: Adjust bamtools location.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (express)[arguments]: Modify location of libbamtools.so in 'use-shared-boost-libs-and-set-bamtools-paths; drop trailing #T.
2023-04-26gnu: python-dendropy: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dendropy)[native-inputs]: Add python-pytest. [arguments]: Add phase 'python-compatibility; remove 'skip-broken-tests; add #:test-flags; do not delete test files. [build-system]: Use pyproject-build-system.
2023-04-25gnu: cwltool: Use pyproject-build-system.Ricardo Wurmus
"setup.py install is deprecated. Use build and pip and other standards-based tools." It then falls back to attempting to install packages via pip. * gnu/packages/bioinformatics.scm (cwltool)[build-system]: Use pyproject-build-system.
2023-04-25gnu: python-schema-salad: Use pyproject-build-system.Ricardo Wurmus
The python-build-system fails with "setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer." This, in turn, causes all Python packages to be ignored and "pip install" to be invoked for them. * gnu/packages/bioinformatics.scm (python-schema-salad)[build-system]: Use pyproject-build-system.
2023-04-25gnu: adapterremoval: Update to 2.3.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (adapterremoval): Update to 2.3.3. [arguments]: Simplify. [inputs]: Reformat.
2023-04-25gnu: bedtools-2.18: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Fix operators in 'compatibility phase.
2023-04-25gnu: hisat: Build with GCC 10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat)[native-inputs]: Add gcc-10.
2023-04-25gnu: kallisto: Update to 0.48.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.48.0. [arguments]: Remove trailing #T from build phase.
2023-04-25gnu: bpp-core: Build with GCC 10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bpp-core)[native-inputs]: Add gcc-10.
2023-04-25gnu: vcflib: Update to 1.0.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.9. [source]: Update snippet. [inputs]: Add curl, pybind11, and wfa2-lib. [arguments]: Adjust and reformat.
2023-04-25gnu: tabixpp: Update to 1.1.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.2. [source]: Simplify snippet. [inputs]: Add curl. [arguments]: Simplify and reformat.
2023-04-25gnu: Add wfa2-lib.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (wfa2-lib): New variable.
2023-04-25gnu: lofreq: Set file timestamps to 1980s.Ricardo Wurmus
This keeps Python from complaining: "ZIP does not support timestamps before 1980". * gnu/packages/bioinformatics.scm (lofreq)[arguments]: Add build phase 'set-source-file-times-to-1980.
2023-04-25gnu: lofreq: Drop input labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (lofreq)[inputs]: Drop package labels.
2023-04-25gnu: ivar: Update to 1.4.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ivar): Update to 1.4.2. [arguments]: Remove -Werror flag.
2023-04-24gnu: multiqc: Update to 1.14.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.14. [build-system]: Use pyproject-build-system. [arguments]: Simplify check phase; restore sanity-check phase. [propagated-inputs]: Add python-rich-click. [native-inputs]: Update test data.
2023-04-24gnu: macs: Patch version check for Python.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (macs)[source]: Patch check for Python > 3.6.
2023-04-24gnu: salmon: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (salmon): Update to 1.10.1. [inputs]: Replace cereal-1.3.0 with cereal; add htscodecs. [native-inputs]: Update hash of pufferfish sources.
2023-04-24gnu: Add htscodecs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htscodecs): New variable.
2023-04-22Merge remote-tracking branch 'origin/master' into core-updatesAndreas Enge
2023-04-21gnu: bppsuite: Update to 2.4.1.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bppsuite): Update to 2.4.1. [source]: Remove the commit and use the release version. Changed to the github repo. [arguments]: Remove the disabled parallel-build. [inputs]: Use list. [home-page]: Changed to github page.
2023-04-21gnu: bpp-popgen: Update to 2.4.1.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bpp-popgen): Update to 2.4.1. [source]: Remove the commit and use the release version. Changed to the github repo. [arguments]: Remove the disabled parallel-build. [home-page]: Changed to new host Université Claude-Bernard Lyon 1.
2023-04-21gnu: Add maffilter.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (maffilter): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-04-21gnu: Add bpp-phyl-omics.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bpp-phyl-omics): New variable.
2023-04-21gnu: Add bpp-seq-omics.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bpp-seq-omics): New variable.
2023-04-21gnu: bpp-phyl: Update to 2.4.1.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bpp-phyl): Update to 2.4.1. [source]: Remove the commit and use the release version. Changed to the github repo. [arguments]: Remove the disabled parallel-build and out-of-source. [home-page]: Changed to new host Université Claude-Bernard Lyon 1. [synopsis]: Use proper capitalization.
2023-04-21gnu: bpp-seq: Update to 2.4.1.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bpp-seq): Update to 2.4.1. [source]: Remove the commit and use the release version. Changed to the github repo. [arguments]: Remove the disabled parallel-build and out-of-source. [home-page]: Changed to new host Université Claude-Bernard Lyon 1.
2023-04-21gnu: bpp-core: Update to 2.4.1.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (bpp-core): Update to 2.4.1. [source]: Remove the commit and use the release version. Changed to the github stored sources. [arguments]: Remove the disabled parallel-build. [home-page]: Changed to new host Université Claude-Bernard Lyon 1.
2023-04-17Merge remote-tracking branch 'origin/master' into core-updatesAndreas Enge
2023-04-17gnu: Add r-demuxmix.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-demuxmix): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-04-17gnu: Add r-demultiplex2.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-demultiplex2): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-04-14Merge branch 'master' into core-updates.Maxim Cournoyer
Conflicts: gnu/local.mk gnu/packages/build-tools.scm gnu/packages/certs.scm gnu/packages/check.scm gnu/packages/compression.scm gnu/packages/cups.scm gnu/packages/fontutils.scm gnu/packages/gnuzilla.scm gnu/packages/guile.scm gnu/packages/ibus.scm gnu/packages/image-processing.scm gnu/packages/linux.scm gnu/packages/music.scm gnu/packages/nss.scm gnu/packages/pdf.scm gnu/packages/python-xyz.scm gnu/packages/qt.scm gnu/packages/ruby.scm gnu/packages/shells.scm gnu/packages/tex.scm gnu/packages/video.scm gnu/packages/vulkan.scm gnu/packages/web.scm gnu/packages/webkit.scm gnu/packages/wm.scm
2023-04-07gnu: Purge pre-1.3.0 deprecated packages.Bruno Victal
* gnu/packages/bioinformatics.scm (deeptools): Remove variable. * gnu/packages/efi.scm (efi_analyzer): Ditto. * gnu/packages/guile.scm (guile-2.2/bug-fix, guile-json): Ditto. * gnu/packages/image.scm (libjpeg): Ditto. * gnu/packages/kde.scm (kdevplatform): Ditto * gnu/packages/linphone.scm (linphoneqt): Ditto. * gnu/packages/maths.scm (blis-sandybridge, blis-haswell, blis-knl): Ditto. * gnu/packages/mpi.scm (hwloc-2.0): Ditto. * gnu/packages/music.scm (python-abjad, zlfo): Ditto. * gnu/packages/perl.scm (perl-base, perl-parent): Ditto. * gnu/packages/tryton.scm (python-trytond): Ditto. * gnu/packages/video.scm (gnome-mpv): Ditto. * tests/graph.scm: Use guile-json-1. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-03-30gnu: Add r-maxprobes.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-maxprobes): New variable.
2023-03-30gnu: Add r-illuminahumanmethylationepicanno-ilm10b5-hg38.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-illuminahumanmethylationepicanno-ilm10b5-hg38): New variable.
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