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2754 Commits

Author SHA1 Message Date
Efraim Flashner
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
Maxim Cournoyer
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
Ricardo Wurmus
c4a2cbeb06
gnu: Add r-demultiplex. 
* gnu/packages/bioinformatics.scm (r-demultiplex): New variable.
 2021-01-28 22:24:51 +01:00
Ricardo Wurmus
04b1a1f6bd
gnu: Add repeat-masker. 
* gnu/packages/bioinformatics.scm (repeat-masker): New variable.
 2021-01-28 15:07:55 +01:00
Ricardo Wurmus
6d3cafa086
gnu: Add trf. 
* gnu/packages/bioinformatics.scm (trf): New variable.
 2021-01-28 15:07:55 +01:00
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Mădălin Ionel Patrașcu
c0afd8044f
gnu: Add r-snapatac. 
* gnu/packages/bioinformatics.scm (r-snapatac): New variable.
 2021-01-18 23:26:53 +01:00
Mădălin Ionel Patrașcu
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
Efraim Flashner
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
Efraim Flashner
9b6cddd32d
gnu: Add ruby-bio-vcf. 
* gnu/packages/bioinformatics.scm (ruby-bio-vcf): New variable.
 2021-01-18 10:41:46 +02:00
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
daf96e704d
gnu: gemma: Add Texinfo markup. 
* gnu/packages/bioinformatics.scm (gemma)[description]: Use Texinfo
markup.
 2021-01-14 20:43:30 +02:00
Efraim Flashner
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
zimoun
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
zimoun
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
zimoun
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
zimoun
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
zimoun
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
zimoun
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
zimoun
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
zimoun
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
zimoun
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
zimoun
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
Marius Bakke
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
Marius Bakke
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
4617cc7fd5
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.
 2020-12-09 12:12:48 +01:00
zimoun
cde035e67f
gnu: r-gqtlstats: Update to 1.21.3. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.21.3.
 2020-12-09 12:12:48 +01:00
zimoun
6a4818716d
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.
 2020-12-09 12:12:48 +01:00
zimoun
970984237a
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>.
 2020-12-09 12:12:47 +01:00
zimoun
53affb349a
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>.
 2020-12-09 12:12:46 +01:00
Ricardo Wurmus
86fcceeae1
gnu: Add r-rhdf5filters. 
* gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable.
 2020-12-09 12:12:46 +01:00
zimoun
60ad3c7b3b
gnu: r-genomationdata: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.22.0.
 2020-12-09 12:12:46 +01:00
zimoun
e707820442
gnu: r-sushi: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.28.0.
 2020-12-09 12:12:45 +01:00
zimoun
83129edfb7
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.
 2020-12-09 12:12:45 +01:00
zimoun
717e53fdc0
gnu: r-gviz: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.34.0.
 2020-12-09 12:12:45 +01:00
zimoun
0a8d08e887
gnu: r-ldblock: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.20.0.
 2020-12-09 12:12:45 +01:00
zimoun
494010ad3e
gnu: r-erma: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.6.0.
 2020-12-09 12:12:45 +01:00
zimoun
6e338901bf
gnu: r-snpstats: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.40.0.
 2020-12-09 12:12:45 +01:00
zimoun
74a11b21be
gnu: r-ggbio: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.38.0.
 2020-12-09 12:12:45 +01:00
zimoun
3c6eecdeed
gnu: r-biovizbase: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.38.0.
 2020-12-09 12:12:45 +01:00
zimoun
6e182c237a
gnu: r-organismdbi: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.32.0.
 2020-12-09 12:12:44 +01:00
zimoun
06fe3b7a53
gnu: r-ensembldb: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.0.
 2020-12-09 12:12:44 +01:00
zimoun
8962a13afe
gnu: r-dirichletmultinomial: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.32.0.
 2020-12-09 12:12:44 +01:00
Roel Janssen
4ef1e375b4
gnu: r-complexheatmap: Update to 2.6.2. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.6.2;
[propagated-inputs]: Add r-cairo, r-digest, r-iranges, r-matrixstats, and
r-s4vectors.
 2020-12-09 12:12:44 +01:00
zimoun
0fde2f9ad2
gnu: r-genomicfiles: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.26.0.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:44 +01:00
zimoun
78cadd0fef
gnu: r-gage: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.0.
 2020-12-09 12:12:44 +01:00
zimoun
143437c623
gnu: r-keggrest: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.0.
 2020-12-09 12:12:44 +01:00
zimoun
b6dd0722c8
gnu: r-fastseg: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.36.0.
 2020-12-09 12:12:44 +01:00
zimoun
a9dc755e67
gnu: r-annotationhub: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.0.
 2020-12-09 12:12:43 +01:00
zimoun
3becce3ff3
gnu: r-interactivedisplaybase: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.28.0.
 2020-12-09 12:12:43 +01:00
zimoun
8e55b9f502
gnu: r-edaseq: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.24.0.
 2020-12-09 12:12:43 +01:00
zimoun
8db8a683b9
gnu: r-aroma-light: Update to 3.20.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.20.0.
 2020-12-09 12:12:43 +01:00
zimoun
971f3a377c
gnu: r-msnid: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.24.0.
[propagated-inputs]: Add r-annotationdbi, r-annotationhub, r-biocgenerics,
r-biocstyle, r-biostrings, r-ggplot2, r-msmstests, r-purrr, r-rlang, r-runit,
r-stringr, r-tibble, and r-xtable.
 2020-12-09 12:12:43 +01:00
zimoun
2ed937e0aa
gnu: r-pcamethods: Update to 1.82.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.82.0.
 2020-12-09 12:12:43 +01:00
zimoun
b47560c1cf
gnu: r-mzid: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.28.0.
[propagated-inputs]: Remove r-rcpp.
 2020-12-09 12:12:43 +01:00
zimoun
75bdab83cc
gnu: r-vsn: Update to 3.58.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.58.0.
 2020-12-09 12:12:42 +01:00
zimoun
6a6f38b89e
gnu: r-affy: Update to 1.68.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.68.0.
 2020-12-09 12:12:42 +01:00
zimoun
d6750c6587
gnu: r-affyio: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.60.0.
 2020-12-09 12:12:42 +01:00
Ricardo Wurmus
471ceb5e5e
gnu: r-mzr: Fix linking. 
* gnu/packages/bioinformatics.scm (r-mzr)[arguments]: Fix linking with rhdf5
libraries.
 2020-12-09 12:12:42 +01:00
Ricardo Wurmus
badb4678bd
gnu: r-mzr: Update to 2.24.1. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.24.1.
 2020-12-09 12:12:42 +01:00
zimoun
4d9e168db8
gnu: r-protgenerics: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.22.0.
 2020-12-09 12:12:42 +01:00
zimoun
858eb988a0
gnu: r-sva: Update to 3.38.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.38.0.
 2020-12-09 12:12:42 +01:00
zimoun
99bd4f2d7c
gnu: r-methylkit: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.0.
 2020-12-09 12:12:42 +01:00
zimoun
2ed79a0a42
gnu: r-copywriter: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.22.0.
 2020-12-09 12:12:41 +01:00
zimoun
36fd725b6f
gnu: r-chipseq: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.40.0.
 2020-12-09 12:12:41 +01:00
zimoun
cad3eb4eb4
gnu: r-annotationfilter: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.14.0.
 2020-12-09 12:12:41 +01:00
zimoun
ec0050c0a9
gnu: r-tximport: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.18.0.
 2020-12-09 12:12:41 +01:00
Roel Janssen
6d5a4dd0a7
gnu: r-mutationalpatterns: Update to 3.0.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 3.0.1.
[native-inputs]: Add r-knitr.
[propagated-inputs]: Add r-bsgenome, r-dplyr, r-ggalluvial,
r-magrittr, r-purrr, r-stringr, r-tibble, and r-tidyr; remove
r-reshape2 and r-summarizedexperiment.
 2020-12-09 12:12:41 +01:00
zimoun
a823a74525
gnu: r-rcas: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.16.0.
 2020-12-09 12:12:41 +01:00
zimoun
2c15a1c502
gnu: r-bamsignals: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.22.0.
 2020-12-09 12:12:41 +01:00
zimoun
728369634f
gnu: r-rhtslib: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.22.0.
 2020-12-09 12:12:41 +01:00
zimoun
b0d85e36f1
gnu: r-zlibbioc: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.36.0.
 2020-12-09 12:12:40 +01:00
zimoun
329879b70c
gnu: r-seqlogo: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.56.0.
 2020-12-09 12:12:40 +01:00
zimoun
2a70c96e3d
gnu: r-genomation: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.22.0.
 2020-12-09 12:12:40 +01:00
zimoun
44bf116f03
gnu: r-seqpattern: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.22.0.
 2020-12-09 12:12:40 +01:00
zimoun
a180744b37
gnu: r-impute: Update to 1.64.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.64.0.
 2020-12-09 12:12:40 +01:00
zimoun
e2e11f095f
gnu: r-bsgenome: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.58.0.
 2020-12-09 12:12:40 +01:00
Roel Janssen
6a7de43a58
gnu: r-topgo: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.42.0.
 2020-12-09 12:12:40 +01:00
Roel Janssen
26e2184fc1
gnu: r-genomicfeatures: Update to 1.42.1. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.1.
 2020-12-09 12:12:40 +01:00
zimoun
92377e7fea
gnu: r-rtracklayer: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.50.0.
 2020-12-09 12:12:39 +01:00
zimoun
077e813657
gnu: r-genomicalignments: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.26.0.
 2020-12-09 12:12:39 +01:00
zimoun
3ca5b05474
gnu: r-variantannotation: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.36.0.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:39 +01:00
zimoun
8607a5394b
gnu: r-summarizedexperiment: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.20.0.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:39 +01:00
zimoun
9168ab0911
gnu: r-rsamtools: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.6.0.
 2020-12-09 12:12:39 +01:00
zimoun
5d60273b77
gnu: r-biostrings: Update to 2.58.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.58.0.
 2020-12-09 12:12:39 +01:00
Roel Janssen
444b101dc2
gnu: r-biocparallel: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.24.1.
 2020-12-09 12:12:39 +01:00
zimoun
4fac3fe67d
gnu: r-biomart: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.0.
 2020-12-09 12:12:39 +01:00
zimoun
f517365cef
gnu: r-annotationdbi: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.52.0.
 2020-12-09 12:12:39 +01:00
zimoun
9103041d13
gnu: r-biobase: Update to 2.50.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.50.0.
 2020-12-09 12:12:38 +01:00
zimoun
7641dba3e6
gnu: r-genomicranges: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.42.0.
 2020-12-09 12:12:38 +01:00
zimoun
d972ab690e
gnu: r-limma: Update to 3.46.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.46.0.
 2020-12-09 12:12:38 +01:00
zimoun
5996929b36
gnu: r-edger: Update to 3.32.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.0.
 2020-12-09 12:12:38 +01:00
zimoun
cde7fcedf9
gnu: r-genomeinfodb: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.0.
 2020-12-09 12:12:38 +01:00
zimoun
2ae3b7db24
gnu: r-bioccheck: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.26.0.
 2020-12-09 12:12:38 +01:00
zimoun
1160c83caf
gnu: r-biocstyle: Update to 2.18.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.0.
 2020-12-09 12:12:38 +01:00
zimoun
182a080127
gnu: r-biocviews: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.0.
 2020-12-09 12:12:38 +01:00
zimoun
16a4822a07
gnu: r-grohmm: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.24.0.
 2020-12-09 12:12:37 +01:00
Roel Janssen
5598f53497
gnu: r-systempiper: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.2.
[propagated-inputs]: Add r-iranges.
 2020-12-09 12:12:37 +01:00
zimoun
a05bb428e4
gnu: r-shortread: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.48.0.
 2020-12-09 12:12:37 +01:00
zimoun
74204b48eb
gnu: r-gostats: Update to 2.56.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.56.0.
 2020-12-09 12:12:37 +01:00
zimoun
afbc8e1433
gnu: r-category: Update to 2.56.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.56.0.
 2020-12-09 12:12:37 +01:00
zimoun
03312f052a
gnu: r-gseabase: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.0.
 2020-12-09 12:12:37 +01:00
zimoun
7a57b229b6
gnu: r-rbgl: Update to 1.66.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.66.0.
 2020-12-09 12:12:37 +01:00
zimoun
4451918e3a
gnu: r-annotationforge: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.32.0.
 2020-12-09 12:12:37 +01:00
zimoun
a323c1e9b4
gnu: r-dexseq: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.36.0.
 2020-12-09 12:12:37 +01:00
zimoun
936227f144
gnu: r-deseq2: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.30.0.
 2020-12-09 12:12:37 +01:00
zimoun
64cf667e98
gnu: r-genefilter: Update to 1.72.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.0.
 2020-12-09 12:12:36 +01:00
zimoun
fafa94b065
gnu: r-delayedarray: Update to 0.16.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.0.
[propagated-inputs]: Add r-matrixgenerics; remove r-matrixstats.
 2020-12-09 12:12:36 +01:00
zimoun
cf6033ee6e
gnu: r-iranges: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.0.
 2020-12-09 12:12:35 +01:00
zimoun
57820475db
gnu: r-s4vectors: Update to 0.28.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.0.
 2020-12-09 12:12:35 +01:00
zimoun
724b770678
gnu: r-xvector: Update to 0.30.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.30.0.
 2020-12-09 12:12:35 +01:00
zimoun
1e536c307c
gnu: Update r-msnbase to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.0.
 2020-12-09 12:12:27 +01:00
Efraim Flashner
3832704aff
gnu: minimap2: Fix build on aarch64-linux. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust
configure-flags to be better per-architecture.
[source]: Add patch.
* gnu/packages/patches/minimap2-aarch64-support.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2020-12-07 12:48:07 +02:00
Efraim Flashner
f48cd014f3
gnu: minimap2: Prepare for cross compilation. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Use
cc-for-target.
 2020-12-07 12:48:01 +02:00
Ricardo Wurmus
555677fdf7
gnu: java-picard-1.113: Use ant/java8. 
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use
ant/java8.
[inputs]: Replace ant with ant/java8.
 2020-12-01 13:30:34 +01:00
Ricardo Wurmus
80fbad4fe6
gnu: pigx-chipseq: Update to 0.0.51. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.51.
[inputs]: Add r-corrplot, r-deseq2, r-dt, r-ggrepel, r-gprofiler2, r-pheatmap,
and r-rsubread.
 2020-11-30 22:39:34 +01:00
Ricardo Wurmus
d3c1b5f66d
gnu: pigx-scrnaseq: Update to 1.1.7. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.7.
 2020-11-30 22:39:34 +01:00
Marius Bakke
bff94a5a53
Merge branch 'master' into staging 2020-11-26 01:08:35 +01:00
Maxim Cournoyer
4efbf56e53
gnu: tadbit: Update to 1.0.1. 
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1.
[arguments]: Remove #:tests? and #:python arguments.
[phases]{fix-problems-with-setup.py}: Remove no longer needed steps.
{check}: Override phase.
[native-inputs]: Add glib and pkg-config.
[inputs]: Add python-future and python-h5py.
 2020-11-24 02:20:32 -05:00
Maxim Cournoyer
e7e73f750f
gnu: imp: Migrate to Python 3. 
* gnu/packages/bioinformatics.scm (imp)
[arguments]: Enable tests by removing the #:tests? argument.
Specify the arguments to pass to the ctest test running via the
 #:configure-flags argument.
[inputs]: Add cgal and opencv.  Remove python-2.  Move swig to...
[native-inputs]: ...here.  Add python-wrapper.
[propagated-inputs]: Replace python2-numpy, python2-scipy, python2-pandas,
python2-scikit-learn and python2-networkx by python-numpy, python-scipy,
python-pandas, python-scikit-learn and python-networkx, respectively.
 2020-11-24 02:20:31 -05:00
Marius Bakke
87a027243f
Merge branch 'master' into staging 2020-11-23 23:39:47 +01:00
Efraim Flashner
964bc9e5fe
gnu: Add cwltool. 
* gnu/packages/bioinformatics.scm (cwltool): New variable.
 2020-11-23 15:43:38 +02:00
Efraim Flashner
7face25953
gnu: Add python-schema-salad. 
* gnu/packages/bioinformatics.scm (python-schema-salad): New variable.
 2020-11-23 15:43:37 +02:00
Marius Bakke
4e5e05d409
Merge branch 'master' into staging 2020-11-15 23:45:34 +01:00
Ricardo Wurmus
e1fa3ea9fe
gnu: methyldackel: Update to 0.5.1. 
* gnu/packages/bioinformatics.scm (methyldackel): Update to 0.5.1.
[arguments]: Link with libbigwig.
[inputs]: Add curl and libbigwig; replace htslib with htslib-1.9.
 2020-11-15 23:31:35 +01:00
Roel Janssen
37ba374a53
gnu: Fix build for python-pysam. 
* gnu/packages/bioinformatics.scm (python-pysam): Use htslib-1.9,
  samtools-1.9, and bcftools-1.9.
 2020-11-13 16:16:43 +01:00
Roel Janssen
ecc309c142
gnu: Add bcftools-1.9. 
* gnu/packages/bioinformatics.scm (bcftools-1.9): New variable.
 2020-11-13 16:14:01 +01:00
Roel Janssen
c3232fcc77
gnu: bedtools: Use samtools-1.9. 
The build for bedtools with samtools 1.11 triggers a testsuite
failure which is reported here:
https://github.com/arq5x/bedtools2/issues/814

* gnu/packages/bioinformatics.scm (bedtools): Use samtools-1.9.
 2020-11-13 14:49:31 +01:00
Roel Janssen
da4a38edad
gnu: Add samtools-1.9. 
* gnu/packages/bioinformatics.scm (samtools-1.9): New variable.
 2020-11-13 14:49:27 +01:00
Roel Janssen
3ede804f6d
gnu: Add htslib-1.9. 
* gnu/packages/bioinformatics.scm (htslib-1.9): New variable.
 2020-11-13 14:49:20 +01:00
Marius Bakke
a9a0d34874
Merge branch 'master' into staging 2020-11-11 00:02:32 +01:00
Efraim Flashner
4b3a535770
gnu: macs: Remove generated code. 
* gnu/packages/bioinformatics.scm (macs)[source]: Add snippet to remove
cython generated code.
[native-inputs]: Add python-cython.
 2020-11-09 11:34:08 +02:00
Efraim Flashner
4dcd19d3ff
gnu: macs: Update check phase. 
* gnu/packages/bioinformatics.scm (macs)[arguments]: Don't delete 'check
phase before using custom 'check phase.
 2020-11-09 11:34:08 +02:00
Efraim Flashner
fa82adb5e0
gnu: macs: Update source, home-page URIs. 
* gnu/packages/bioinformatics.scm (macs)[source, home-page]: Update
URIs to new location.
 2020-11-09 11:34:08 +02:00
Marius Bakke
32787d6524
Merge branch 'master' into staging 
Conflicts:
	gnu/local.mk
	gnu/packages/gdb.scm
	gnu/packages/lisp-xyz.scm
	gnu/packages/web-browsers.scm
 2020-11-07 21:33:32 +01:00
Roel Janssen
bcbd536e3f
gnu: Update samtools to 1.11. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.11.
 2020-10-29 16:55:07 +01:00
Roel Janssen
04a49b4143
gnu: Update bcftools to 1.11. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.11.
 2020-10-29 16:55:03 +01:00
Roel Janssen
f40add4dbb
gnu: Update htslib to 1.11. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.11.
 2020-10-29 16:54:55 +01:00