| Age | Commit message (Expand) | Author |
|---|
| 2023-05-08 | gnu: Add homer.•••* gnu/packages/bioinformatics.scm (homer): New variable.
| Ricardo Wurmus |
| 2023-05-05 | Revert "gnu: Add python-gimmemotifs."•••This reverts commit dc8b3ebe5d4ba2a39c12f62d836963ffee1e4b47.
python-gimmemotifs is not usable without proprietary third-party tools.
| Ricardo Wurmus |
| 2023-05-05 | gnu: Add python-gimmemotifs.•••* gnu/packages/bioinformatics.scm (python-gimmemotifs): New variable.
| Ricardo Wurmus |
| 2023-05-05 | gnu: Add python-biofluff.•••* gnu/packages/bioinformatics.scm (python-biofluff): New variable.
| Ricardo Wurmus |
| 2023-05-05 | gnu: Add python-genomepy.•••* gnu/packages/bioinformatics.scm (python-genomepy): New variable.
| Ricardo Wurmus |
| 2023-05-05 | gnu: Add python-logomaker.•••* gnu/packages/bioinformatics.scm (python-logomaker): New variable.
| Ricardo Wurmus |
| 2023-05-05 | gnu: python-pyfaidx: Update to 0.7.2.1.•••* 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.
| Ricardo Wurmus |
| 2023-05-04 | gnu: python-screed: Update to 1.1.2.•••* 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>
| Mădălin Ionel Patrașcu |
| 2023-05-04 | gnu: Add python-goatools.•••* gnu/packages/bioinformatics.scm (python-goatools): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-05-03 | gnu: pigx-sars-cov-2: Update to 0.0.9.•••* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.9.
| Ricardo Wurmus |
| 2023-05-03 | gnu: Add fanc.•••* gnu/packages/bioinformatics.scm (fanc): New variable.
| Ricardo Wurmus |
| 2023-04-29 | gnu: r-tictoc: Update to 1.2.•••* gnu/packages/bioinformatics.scm (r-tictoc): Update to 1.2.
| Ricardo Wurmus |
| 2023-04-27 | gnu: gdcm: Disable dependent tests.•••* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Disable tests that depend
on the output of a disabled test.
| Ricardo Wurmus |
| 2023-04-27 | gnu: freebayes: Update to 1.3.7.•••* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.7.
[arguments]: Do not use "grep -P" in tests; drop trailing #T.
| Ricardo Wurmus |
| 2023-04-27 | gnu: vcflib: Use libwfa2.pc.•••* 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.
| Ricardo Wurmus |
| 2023-04-27 | gnu: wfa2-lib: Install pkg-config file.•••* gnu/packages/bioinformatics.scm (wfa2-lib)[arguments]: Install libwfa2.pc.
| Ricardo Wurmus |
| 2023-04-27 | gnu: express: Adjust bamtools location.•••* gnu/packages/bioinformatics.scm (express)[arguments]: Modify location of
libbamtools.so in 'use-shared-boost-libs-and-set-bamtools-paths; drop trailing
#T.
| Ricardo Wurmus |
| 2023-04-26 | gnu: python-dendropy: Fix build.•••* 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.
| Ricardo Wurmus |
| 2023-04-25 | gnu: cwltool: Use pyproject-build-system.•••"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.
| Ricardo Wurmus |
| 2023-04-25 | gnu: python-schema-salad: Use pyproject-build-system.•••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.
| Ricardo Wurmus |
| 2023-04-25 | gnu: adapterremoval: Update to 2.3.3.•••* gnu/packages/bioinformatics.scm (adapterremoval): Update to 2.3.3.
[arguments]: Simplify.
[inputs]: Reformat.
| Ricardo Wurmus |
| 2023-04-25 | gnu: bedtools-2.18: Fix build.•••* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Fix operators in
'compatibility phase.
| Ricardo Wurmus |
| 2023-04-25 | gnu: hisat: Build with GCC 10.•••* gnu/packages/bioinformatics.scm (hisat)[native-inputs]: Add gcc-10.
| Ricardo Wurmus |
| 2023-04-25 | gnu: kallisto: Update to 0.48.0.•••* gnu/packages/bioinformatics.scm (kallisto): Update to 0.48.0.
[arguments]: Remove trailing #T from build phase.
| Ricardo Wurmus |
| 2023-04-25 | gnu: bpp-core: Build with GCC 10.•••* gnu/packages/bioinformatics.scm (bpp-core)[native-inputs]: Add gcc-10.
| Ricardo Wurmus |
| 2023-04-25 | gnu: vcflib: Update to 1.0.9.•••* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.9.
[source]: Update snippet.
[inputs]: Add curl, pybind11, and wfa2-lib.
[arguments]: Adjust and reformat.
| Ricardo Wurmus |
| 2023-04-25 | gnu: tabixpp: Update to 1.1.2.•••* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.2.
[source]: Simplify snippet.
[inputs]: Add curl.
[arguments]: Simplify and reformat.
| Ricardo Wurmus |
| 2023-04-25 | gnu: Add wfa2-lib.•••* gnu/packages/bioinformatics.scm (wfa2-lib): New variable.
| Ricardo Wurmus |
| 2023-04-25 | gnu: lofreq: Set file timestamps to 1980s.•••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.
| Ricardo Wurmus |
| 2023-04-25 | gnu: lofreq: Drop input labels.•••* gnu/packages/bioinformatics.scm (lofreq)[inputs]: Drop package labels.
| Ricardo Wurmus |
| 2023-04-25 | gnu: ivar: Update to 1.4.2.•••* gnu/packages/bioinformatics.scm (ivar): Update to 1.4.2.
[arguments]: Remove -Werror flag.
| Ricardo Wurmus |
| 2023-04-24 | gnu: multiqc: Update to 1.14.•••* 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.
| Ricardo Wurmus |
| 2023-04-24 | gnu: macs: Patch version check for Python.•••* gnu/packages/bioinformatics.scm (macs)[source]: Patch check for Python >
3.6.
| Ricardo Wurmus |
| 2023-04-24 | gnu: salmon: Update to 1.10.1.•••* 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.
| Ricardo Wurmus |
| 2023-04-24 | gnu: Add htscodecs.•••* gnu/packages/bioinformatics.scm (htscodecs): New variable.
| Ricardo Wurmus |
| 2023-04-22 | Merge remote-tracking branch 'origin/master' into core-updates | Andreas Enge |
| 2023-04-21 | gnu: bppsuite: Update to 2.4.1.•••* 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.
| Mădălin Ionel Patrașcu |
| 2023-04-21 | gnu: bpp-popgen: Update to 2.4.1.•••* 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.
| Mădălin Ionel Patrașcu |
| 2023-04-21 | gnu: Add maffilter.•••* gnu/packages/bioinformatics.scm (maffilter): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2023-04-21 | gnu: Add bpp-phyl-omics.•••* gnu/packages/bioinformatics.scm (bpp-phyl-omics): New variable.
| Mădălin Ionel Patrașcu |
| 2023-04-21 | gnu: Add bpp-seq-omics.•••* gnu/packages/bioinformatics.scm (bpp-seq-omics): New variable.
| Mădălin Ionel Patrașcu |
| 2023-04-21 | gnu: bpp-phyl: Update to 2.4.1.•••* 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.
| Mădălin Ionel Patrașcu |
| 2023-04-21 | gnu: bpp-seq: Update to 2.4.1.•••* 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.
| Mădălin Ionel Patrașcu |
| 2023-04-21 | gnu: bpp-core: Update to 2.4.1.•••* 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.
| Mădălin Ionel Patrașcu |
| 2023-04-17 | Merge remote-tracking branch 'origin/master' into core-updates | Andreas Enge |
| 2023-04-17 | gnu: Add r-demuxmix.•••* gnu/packages/bioinformatics.scm (r-demuxmix): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-04-17 | gnu: Add r-demultiplex2.•••* gnu/packages/bioinformatics.scm (r-demultiplex2): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-04-14 | Merge branch 'master' into core-updates.•••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
| Maxim Cournoyer |
| 2023-04-07 | gnu: Purge pre-1.3.0 deprecated packages.•••* 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>
| Bruno Victal |
| 2023-03-30 | gnu: Add r-maxprobes.•••* gnu/packages/bioinformatics.scm (r-maxprobes): New variable.
| Ricardo Wurmus |
