160e4a95e7
gnu: bowtie1: Update to 1.3.0.
...
* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.3.0.
[arguments]: Set CC in make flags.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-02-11 22:29:37 +01:00
0e3e26ca60
gnu: r-gage: Update to 2.40.1.
...
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.1.
2021-02-11 21:33:38 +01:00
5103da059a
gnu: r-msnbase: Update to 2.16.1.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.1.
2021-02-11 21:33:38 +01:00
2596200514
gnu: r-methylkit: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.1.
2021-02-11 21:33:38 +01:00
3f7e96acc7
gnu: r-delayedarray: Update to 0.16.1.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.1.
2021-02-11 21:33:38 +01:00
9b66b8017d
gnu: r-biomart: Update to 2.46.3.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.3.
2021-02-11 21:33:38 +01:00
8e25b1acf9
gnu: r-edger: Update to 3.32.1.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.1.
2021-02-11 21:33:38 +01:00
809f725977
gnu: r-iranges: Update to 2.24.1.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.1.
2021-02-11 21:33:37 +01:00
88fd569ddf
gnu: r-s4vectors: Update to 0.28.1.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.1.
2021-02-11 21:33:37 +01:00
babb2dce34
gnu: r-systempiper: Update to 1.24.3.
...
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.3.
2021-02-11 21:33:37 +01:00
d3ac91dd9d
gnu: r-gseabase: Update to 1.52.1.
...
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.1.
2021-02-11 21:33:37 +01:00
074d142ab6
gnu: r-genefilter: Update to 1.72.1.
...
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.1.
2021-02-11 21:33:37 +01:00
8d61539883
gnu: rsem: Link with shared libhts library.
...
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Link with libhts.so
instead of libhts.a.
2021-02-05 23:30:43 +01:00
877ab0266c
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.
2021-02-01 19:02:14 +02:00
23a5dcce1d
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.
2021-01-29 10:58:25 -05:00
c4a2cbeb06
gnu: Add r-demultiplex.
...
* gnu/packages/bioinformatics.scm (r-demultiplex): New variable.
2021-01-28 22:24:51 +01:00
04b1a1f6bd
gnu: Add repeat-masker.
...
* gnu/packages/bioinformatics.scm (repeat-masker): New variable.
2021-01-28 15:07:55 +01:00
6d3cafa086
gnu: Add trf.
...
* gnu/packages/bioinformatics.scm (trf): New variable.
2021-01-28 15:07:55 +01:00
b3e39a475f
gnu: freebayes: Update source, home-page URIs.
...
* gnu/packages/bioinformatics.scm (freebayes)[source]: Update to new
upstream URI.
[home-page]: Same.
2021-01-19 11:48:38 +02:00
99043adf46
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.
2021-01-19 11:41:07 +02:00
1bbfe1789d
gnu: vcflib: Add pkg-config file.
...
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
create pkg-config file.
2021-01-19 11:36:01 +02:00
d6a8148c8d
gnu: vcflib: Build a shared library.
...
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
build a shared library instead of a static one.
2021-01-19 10:43:06 +02:00
797585746b
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.
2021-01-19 10:33:19 +02:00
c0afd8044f
gnu: Add r-snapatac.
...
* gnu/packages/bioinformatics.scm (r-snapatac): New variable.
2021-01-18 23:26:53 +01:00
2d9c6542c8
gnu: mafft: Update to 7.475.
...
* gnu/packages/bioinformatics.scm (mafft): Update to 7.475.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-01-18 11:57:28 +02:00
6cb86e23a9
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.
2021-01-18 11:19:37 +02:00
9b6cddd32d
gnu: Add ruby-bio-vcf.
...
* gnu/packages/bioinformatics.scm (ruby-bio-vcf): New variable.
2021-01-18 10:41:46 +02:00
fc9fd5496f
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.
2021-01-17 15:47:32 +02:00
3ddeefe854
gnu: multichoose: Install header files.
...
* gnu/packages/bioinformatics.scm (multichoose)[arguments]: Adjust
'install phase to also install header files.
2021-01-17 15:47:32 +02:00
976603b909
gnu: filevercmp: Install header files.
...
* gnu/packages/bioinformatics.scm (filevercmp)[arguments]: Adjust
'install phase to install header files.
2021-01-17 15:47:32 +02:00
93309e25c7
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.
2021-01-14 20:43:31 +02:00
db30d6eada
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.
2021-01-14 20:43:31 +02:00
2051be4f4c
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.
2021-01-14 20:43:31 +02:00
daf96e704d
gnu: gemma: Add Texinfo markup.
...
* gnu/packages/bioinformatics.scm (gemma)[description]: Use Texinfo
markup.
2021-01-14 20:43:30 +02:00
a36abbe005
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.
2021-01-14 20:43:30 +02:00
610cd6a170
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.
2020-12-29 17:40:28 +01:00
81f481d6cd
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.
2020-12-29 17:40:28 +01:00
61ec8928c7
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.
2020-12-29 17:40:28 +01:00
a2c66d18a5
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'.
2020-12-29 17:40:28 +01:00
8c2b7c9a2a
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.
2020-12-29 17:40:28 +01:00
8f1237c350
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.
2020-12-29 17:40:28 +01:00
9534e7b706
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.
2020-12-29 17:40:28 +01:00
2a4322f7c3
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.
2020-12-29 17:40:28 +01:00
69a5e066c1
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.
2020-12-29 17:40:28 +01:00
838db0de5e
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.
2020-12-29 17:40:25 +01:00
6203b8e5bd
gnu: kentutils: Build with OpenSSL 1.1.
...
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL-1.0
to OPENSSL.
2020-12-20 16:30:42 +01:00
ca27b0e528
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.
2020-12-20 16:30:42 +01:00
48f77ecbb1
gnu: r-keggrest: Update to 1.30.1.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.1.
2020-12-09 23:30:12 +01:00
4745f0dfca
gnu: r-genomeinfodb: Update to 1.26.2.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.2.
2020-12-09 23:30:12 +01:00
baeaa02e75
gnu: r-biocstyle: Update to 2.18.1.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.1.
2020-12-09 23:30:12 +01:00
Mădălin Ionel Patrașcu
Ricardo Wurmus
Efraim Flashner
Maxim Cournoyer
zimoun
Marius Bakke