| Age | Commit message (Expand) | Author |
|---|
| 2021-02-05 | gnu: rsem: Link with shared libhts library....* gnu/packages/bioinformatics.scm (rsem)[arguments]: Link with libhts.so
instead of libhts.a.
| Ricardo Wurmus |
| 2021-02-01 | gnu: vcflib: Fix generated pkg-config file....* 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.
| Efraim Flashner |
| 2021-01-29 | gnu: grocsvs: Remove package....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.
| Maxim Cournoyer |
| 2021-01-28 | gnu: Add r-demultiplex....* gnu/packages/bioinformatics.scm (r-demultiplex): New variable.
| Ricardo Wurmus |
| 2021-01-28 | gnu: Add repeat-masker....* gnu/packages/bioinformatics.scm (repeat-masker): New variable.
| Ricardo Wurmus |
| 2021-01-28 | gnu: Add trf....* gnu/packages/bioinformatics.scm (trf): New variable.
| Ricardo Wurmus |
| 2021-01-19 | gnu: freebayes: Update source, home-page URIs....* gnu/packages/bioinformatics.scm (freebayes)[source]: Update to new
upstream URI.
[home-page]: Same.
| Efraim Flashner |
| 2021-01-19 | gnu: freebayes: Don't include vcflib sources....* 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.
| Efraim Flashner |
| 2021-01-19 | gnu: vcflib: Add pkg-config file....* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
create pkg-config file.
| Efraim Flashner |
| 2021-01-19 | gnu: vcflib: Build a shared library....* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
build a shared library instead of a static one.
| Efraim Flashner |
| 2021-01-19 | gnu: freebayes: Extend test timeout on slower architectures....* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Use custom
'check phase on aarch64-linux and armhf-linux to extend the test timeout.
| Efraim Flashner |
| 2021-01-18 | gnu: Add r-snapatac....* gnu/packages/bioinformatics.scm (r-snapatac): New variable.
| Mădălin Ionel Patrașcu |
| 2021-01-18 | gnu: mafft: Update to 7.475....* gnu/packages/bioinformatics.scm (mafft): Update to 7.475.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Mădălin Ionel Patrașcu |
| 2021-01-18 | gnu: ruby-bio-vcf: Rename to bio-vcf....This package is widely known in select circles specifically as 'bio-vcf'.
* gnu/packages/bioinformatics.scm (ruby-bio-vcf): Rename to bio-vcf.
| Efraim Flashner |
| 2021-01-18 | gnu: Add ruby-bio-vcf....* gnu/packages/bioinformatics.scm (ruby-bio-vcf): New variable.
| Efraim Flashner |
| 2021-01-17 | gnu: freebayes: Update to 1.3.3....* 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.
| Efraim Flashner |
| 2021-01-17 | gnu: multichoose: Install header files....* gnu/packages/bioinformatics.scm (multichoose)[arguments]: Adjust
'install phase to also install header files.
| Efraim Flashner |
| 2021-01-17 | gnu: filevercmp: Install header files....* gnu/packages/bioinformatics.scm (filevercmp)[arguments]: Adjust
'install phase to install header files.
| Efraim Flashner |
| 2021-01-14 | gnu: vcflib: Update to 1.0.2....* 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.
| Efraim Flashner |
| 2021-01-14 | gnu: sambamba Update to 0.8.0....* 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.
| Efraim Flashner |
| 2021-01-14 | gnu: gemma: Enable tests....* 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.
| Efraim Flashner |
| 2021-01-14 | gnu: gemma: Add Texinfo markup....* gnu/packages/bioinformatics.scm (gemma)[description]: Use Texinfo
markup.
| Efraim Flashner |
| 2021-01-14 | gnu: gemma: Update to 0.98.3....* 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.
| Efraim Flashner |
| 2020-12-29 | gnu: r-ggbio: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-ggbio): Move from here...
* gnu/packages/bioconductor.scm (r-ggbio): ...to here.
| zimoun |
| 2020-12-29 | gnu: r-gqtlstats: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
| zimoun |
| 2020-12-29 | gnu: r-snpstats: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-snpstats): Move from here...
* gnu/packages/bioconductor.scm (r-snpstats): ...to here.
| zimoun |
| 2020-12-29 | gnu: r-homo-sapiens: Move to (gnu packages bioconductor)....* 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'.
| zimoun |
| 2020-12-29 | gnu: r-erma: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-erma): Move from here...
* gnu/packages/bioconductor.scm (r-erma): ...to here.
| zimoun |
| 2020-12-29 | gnu: r-ldblock: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-ldblock): Move from here...
* gnu/packages/bioconductor.scm (r-ldblock): ...to here.
| zimoun |
| 2020-12-29 | gnu: r-gqtlstats: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
| zimoun |
| 2020-12-29 | gnu: r-gviz: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-gviz): Move from here...
* gnu/packages/bioconductor.scm (r-gviz): ...to here.
| zimoun |
| 2020-12-29 | gnu: r-gwascat: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-gwascat): Move from here...
* gnu/packages/bioconductor.scm (r-gwascat): ...to here.
| zimoun |
| 2020-12-29 | gnu: r-sushi: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-sushi): Move from here...
* gnu/packages/bioconductor.scm (r-sushi): ...to here.
| zimoun |
| 2020-12-20 | gnu: kentutils: Build with OpenSSL 1.1....* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL-1.0
to OPENSSL.
| Marius Bakke |
| 2020-12-20 | gnu: kentutils: Add a file name for the "samtabix" input....* gnu/packages/bioinformatics.scm (kentutils)[native-inputs]: For "samtabix",
add a file name on the origin.
| Marius Bakke |
| 2020-12-09 | gnu: r-keggrest: Update to 1.30.1....* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.1.
| Ricardo Wurmus |
| 2020-12-09 | gnu: r-genomeinfodb: Update to 1.26.2....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.2.
| Ricardo Wurmus |
| 2020-12-09 | gnu: r-biocstyle: Update to 2.18.1....* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.1.
| Ricardo Wurmus |
| 2020-12-09 | gnu: r-rhtslib: Propagate zlib....* 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.
| Ricardo Wurmus |
| 2020-12-09 | gnu: r-gqtlstats: Update to 1.21.3....* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.21.3.
| zimoun |
| 2020-12-09 | gnu: r-gqtlbase: Update to 1.21.1....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.
| zimoun |
| 2020-12-09 | gnu: r-biocviews: Update to 1.58.1....* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.1.
Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
| zimoun |
| 2020-12-09 | gnu: r-rhdf5: Update to 2.34.0....* 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>.
| zimoun |
| 2020-12-09 | gnu: Add r-rhdf5filters....* gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable.
| Ricardo Wurmus |
| 2020-12-09 | gnu: r-genomationdata: Update to 1.22.0....* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.22.0.
| zimoun |
| 2020-12-09 | gnu: r-sushi: Update to 1.28.0....* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.28.0.
| zimoun |
| 2020-12-09 | gnu: r-gwascat: Update to 2.22.0....* 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.
| zimoun |
| 2020-12-09 | gnu: r-gviz: Update to 1.34.0....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.34.0.
| zimoun |
| 2020-12-09 | gnu: r-ldblock: Update to 1.20.0....* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.20.0.
| zimoun |
| 2020-12-09 | gnu: r-erma: Update to 1.6.0....* gnu/packages/bioinformatics.scm (r-erma): Update to 1.6.0.
| zimoun |
