| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.2.
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* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1.
[source]: Add patch to fix compilation.
[arguments]: Adjust regular expressions modifying 'SConstruct'.
* gnu/packages/patches/metabat-fix-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
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* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
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* gnu/packages/bioinformatics.scm (bcftools): Update to 1.5.
[origin]: Remove fix-makefile patch.
[arguments]: Add configure flags, add LIBS make flag. Do not delete
configure phase.
* gnu/packages/patches/bcftools-fix-makefile.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
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* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
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* gnu/packages/bioinformatics (htslib-1.3): New variable.
(bamm)[inputs]: Replace htslib with htslib-1.3.
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* gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1.
[arguments]: Move Makefile modifications from here ...
[source]: ... to added patch. Adjust patch for update to 1.4.
* gnu/packages/patches/bcftools-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1.
[arguments]: Add '--with-htslib=system' configure flag.
[inputs]: Add htslib.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1.
[inputs]: Add curl, openssl.
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* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases"
syntax.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.
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* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.
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* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Update hash because the tarball changed in place.
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* gnu/packages/bioinformatics.scm (sortmerna)[supported-systems]: New field.
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* gnu/packages/bioinformatics.scm (raxml)[supported-systems]: New field.
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* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases'
syntax.
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* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2.
[inputs]: Add zlib.
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* gnu/packages/bioinformatics.scm (deeptools): Update to 2.5.1.
[arguments]: Remove.
[native-inputs]: Use "python-" instead of "python2-" variants.
[inputs]: Likewise; add python-py2bit.
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* gnu/packages/bioinformatics.scm (python-py2bit): New variable.
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* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre. Add patch.
[arguments]: Replace paths in run_with_lock.c. Configure with pcre.
[inputs]: Add pcre, perl, python.
* gnu/packages/patches/blast+-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
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This reverts commit 18dea67dc3a42d782b34b551304748346f173184.
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* gnu/packages/patches/gemma-intel-compat.patch: New file.
* gnu/packages/bioinformatics.scm (gemma)[source]: Add patch.
[arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures.
* gnu/local.mk (dist_patch_DATA): Register patch.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.
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* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre.
[arguments]: Replace paths in run_with_lock.c. Configure with pcre.
[inputs]: Add pcre, perl, python.
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* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.8.
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* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.15.
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* gnu/packages/bioinformatics.scm (f-seq): New variable.
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* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.
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* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.
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* gnu/packages/bioinformatics.scm (kentutils): New variable.
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* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.7.3.
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* gnu/packages/zip.scm (zip, unzip, zziplib, perl-zip): Move to...
* gnu/packages/compression.scm: ...here.
* gnu/packages/zip.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Unregister deleted file.
* po/packages/POTFILES.in: Unregister deleted file.
* gnu/packages/{audio, avr, bioinformatics, busybox, cdrom, ci, compression,
docbook, documentation, fonts, fpga, game-development, games, gl, gnome,
gnuzilla, graphics, guile, haskell, image, java, kodi, ldc, libreoffice,
markup, maths, mc, monitoring, music, php, pretty-print, python, scheme,
smalltalk, statistics, synergy, tex, textutils, video, web-browsers, xml,
zip}.scm, guix/build-system/{ant, font}.scm, guix/{download, packages}.scm:
Adapt module import.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.
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* gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
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* gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
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* gnu/packages/bioinformatics.scm (gemma)[arguments]: On 32-bit
architectures add 'FORCE_32BIT' flag.
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* gnu/packages/bioinformatics.scm (tadbit): New variable.
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* gnu/packages/bioinformatics.scm (imp): New variable.
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* gnu/packages/bioinformatics.scm (phylip): New variable.
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* gnu/packages/bioinformatics.scm (gess): New variable.
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* gnu/packages/bioinformatics.scm (trim-galore): New variable.
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* gnu/packages/bioinformatics.scm (ritornello): New variable.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
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* gnu/packages/bioinformatics.scm (kaiju): New variable.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.3.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.2.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
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* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
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