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Author SHA1 Message Date
Tim Howes
dcee10506c
gnu: infernal: Update to 1.1.4. 
* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.4.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-03 10:11:51 +02:00
Tim Howes
9f4ffc249f
gnu: hmmer: Update to 3.3.2. 
* gnu/packages/bioinformatics.scm (hmmer): Update to 3.3.2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-03 10:11:51 +02:00
Ricardo Wurmus
f21c711a0f
gnu: kallisto: Update to 0.46.2. 
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.46.2.
[source]: Remove bundled htslib sources.
 2021-03-02 17:06:58 +01:00
Ricardo Wurmus
cc39e9dbdc
gnu: kallisto: Use older htslib. 
* gnu/packages/bioinformatics.scm (kallisto)[inputs]: Use htslib-1.9 instead
of the latest.
 2021-03-02 17:06:58 +01:00
Nicolas Goaziou
3759df574d
gnu: f-seq: Use HTTPS home page URI. 
* gnu/packages/bioinformatics.scm (f-seq)[home-page]: Use HTTPS URI.
 2021-02-28 11:03:56 +01:00
Ricardo Wurmus
5d5bbd6fcc
gnu: Add star-for-pigx. 
This is a follow-up to commit f1f6e49190.

* gnu/packages/bioinformatics.scm (star-for-pigx): New variable.
(pigx-rnaseq, pigx-scrnaseq)[inputs]: Replace star with star-for-pigx.
 2021-02-23 19:40:59 +01:00
Ricardo Wurmus
f1f6e49190
gnu: star: Update to 2.7.8a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.7.8a.
 2021-02-22 21:16:19 +01:00
Ricardo Wurmus
f310b06685
gnu: nanopolish: Fix script wrapping. 
* gnu/packages/bioinformatics.scm (nanopolish)[arguments]: Fix wrap-programs
phase.
[inputs]: Add Guile for wrap-script; add bioperl and perl-getopt-long for Perl
scripts.
 2021-02-19 23:35:04 +01:00
Ricardo Wurmus
15c0cc4aa2
gnu: Add prinseq. 
* gnu/packages/bioinformatics.scm (prinseq): New variable.
 2021-02-19 23:14:59 +01:00
Ricardo Wurmus
80d3150c94
gnu: Add ngshmmalign. 
* gnu/packages/bioinformatics.scm (ngshmmalign): New variable.
 2021-02-19 17:24:52 +01:00
Ricardo Wurmus
8360705948
gnu: Add r-archr. 
* gnu/packages/bioinformatics.scm (r-archr): New variable.
 2021-02-18 16:11:38 +01:00
Ricardo Wurmus
9904a15a4c
gnu: Add indelfixer. 
* gnu/packages/bioinformatics.scm (indelfixer): New variable.
 2021-02-15 13:51:58 +01:00
Mădălin Ionel Patrașcu
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
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
Ludovic Courtès
c9a656a5d0
gnu: imp: Update to 2.13.0. 
* gnu/packages/bioinformatics.scm (imp): Update to 2.13.0.
 2020-10-23 16:35:38 +02:00
Marius Bakke
997abda92b
gnu: Remove redundant MariaDB inputs. 
For well-behaved build systems, including the "dev" output suffices.

* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Remove MARIADB:LIB.
* gnu/packages/cran.scm (r-rmysql)[inputs]: Likewise.
* gnu/packages/databases.scm (python-mysqlclient, soci)[inputs]: Likewise.
* gnu/packages/qt.scm (qt-4, qtbase): Likewise.
* gnu/packages/ruby.scm (ruby-mysql2)[inputs]: Likewise.
 2020-10-13 23:48:16 +02:00
Marius Bakke
f7175626ff
Merge branch 'master' into staging 2020-10-13 23:39:27 +02:00
Roel Janssen
fb0037af8c
gnu: htslib: Enable support for custom URI schemes. 
* gnu/packages/bioinformatics.scm (htslib)[arguments]: Enable support for custom URIs.
 2020-10-07 15:33:28 +02:00
Ricardo Wurmus
73a2fe4ab7
gnu: r-gqtlbase: Update to 1.20.4. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.4.
 2020-10-06 13:23:38 +02:00
Ricardo Wurmus
906c79d1a3
gnu: r-rhdf5: Update to 2.32.3. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.3.
 2020-10-06 13:23:38 +02:00
Ricardo Wurmus
78d9fbd2fd
gnu: r-biocstyle: Update to 2.16.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.1.
 2020-10-06 13:23:38 +02:00
Guillaume Le Vaillant
87c079d9b5
Merge branch 'master' into staging 2020-10-05 14:17:25 +02:00
Mădălin Ionel Patrașcu
0990d61193
gnu: mafft: Update to 7.471. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.471.

Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
 2020-09-25 14:12:13 +02:00
Guillaume Le Vaillant
2374443561
Merge branch 'staging' into wip-lisp 2020-09-23 14:50:19 +02:00
Nicolas Goaziou
d27ec8db70
gnu: mafft: Use HTTPS home page URI. 
* gnu/packages/bioinformatics.scm (mafft)[home-page, license]: Use HTTPS URI.
 2020-09-22 11:12:52 +02:00
zimoun
3292f6eda0
gnu: r-fithic: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-fithic): Move from here...
* gnu/packages/bioconductor.scm (r-fithic): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:40:15 +02:00
zimoun
7df42d3774
gnu: r-hitc: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-hitc): Move from here...
* gnu/packages/bioconductor.scm (r-hitc): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:40:15 +02:00
zimoun
63b75c01c2
gnu: r-hdf5array: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-hdf5array): Move from here...
* gnu/packages/bioconductor.scm (r-hdf5array): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:40:10 +02:00
zimoun
c61268c1b7
gnu: r-rhdf5lib: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:39:33 +02:00
zimoun
8863c14cd8
gnu: r-beachmat: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-beachmat): Move from here...
* gnu/packages/bioconductor.scm (r-beachmat): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:39:30 +02:00
zimoun
916a3e59ab
gnu: r-singlecellexperiment: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Move from here...
* gnu/packages/bioconductor.scm (r-singlecellexperiment): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:39:27 +02:00
zimoun
6b1946b334
gnu: r-scater: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-scater): Move from here...
* gnu/packages/bioconductor.scm (r-scater): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:39:24 +02:00
zimoun
1193b77e60
gnu: r-scran: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-scran): Move from here...
* gnu/packages/bioconductor.scm (r-scran): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:39:22 +02:00
zimoun
8c7c6db408
gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Move from here...
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-14 21:39:19 +02:00
zimoun
d4e2ec1b8a
gnu: r-absfiltergsea: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-absfiltergsea): Move from here...
* gnu/packages/cran.scm (r-absfiltergsea): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-11 21:59:23 +02:00
zimoun
77c7394086
gnu: r-diversitree: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-diversitree): Move from here...
* gnu/packages/cran.scm (r-diversitree): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-11 21:59:23 +02:00
zimoun
415aa8a583
gnu: r-phangorn: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-phangorn): Move from here...
* gnu/packages/cran.scm (r-phangorn): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-11 21:59:21 +02:00
zimoun
f9c0b2e05a
gnu: r-seurat: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-seurat): Move from here...
* gnu/packages/cran.scm (r-seurat): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-11 21:59:17 +02:00
zimoun
b31c364467
gnu: r-maldiquant: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-maldiquant): Move from here...
* gnu/packages/cran.scm (r-maldiquant): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-11 21:59:12 +02:00
zimoun
30aaee3306
gnu: r-seqminer: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-seqminer): Move from here...
* gnu/packages/cran.scm (r-seqminer): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-11 21:59:07 +02:00
zimoun
66a8e62070
gnu: r-qtl2: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-qtl2): Move from here...
* gnu/packages/cran.scm (r-qtl2): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-11 21:59:03 +02:00
zimoun
496a52dc41
gnu: r-qtl: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-qtl): Move from here...
* gnu/packages/cran.scm (r-qtl): ...to here.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-09-11 21:58:58 +02:00
Roel Janssen
66be746dc0
gnu: Move r-bisquerna. 
* gnu/packages/bioinformatics.scm (r-bisquerna): Move to ...
* gnu/packages/cran.scm: ... here.
 2020-09-10 16:38:43 +02:00
Ricardo Wurmus
0f8db4dc88
Revert "gnu: Add r-loomr." 
This reverts commit 1f56ec08af.

This package is not free software.
 2020-09-09 18:14:48 +02:00
Roel Janssen
0574446be8
gnu: Add r-bisquerna. 
* gnu/packages/bioinformatics.scm (r-bisquerna): New variable.
 2020-09-09 17:02:55 +02:00
Roel Janssen
1f56ec08af
gnu: Add r-loomr. 
* gnu/packages/bioinformatics.scm (r-loomr): New variable.
 2020-09-09 16:56:02 +02:00
Andreas Enge
44f93ed6ed
gnu: seqmagick: Update to 0.8.0. 
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.0.
 2020-09-05 22:32:33 +02:00
Efraim Flashner
de3c03a471
Merge remote-tracking branch 'origin/master' into staging 2020-09-05 22:30:04 +03:00
Efraim Flashner
319de44a09
gnu: delly: Update to 0.8.3. 
* gnu/packages/bioinformatics.scm (delly): Update to 0.8.3.
[inputs]: Order alphabetically.
 2020-08-30 22:55:48 +03:00
Efraim Flashner
e8bbb29b59
gnu: vcflib: Install pkgconfig file. 
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Adjust custom
'install phase to add vcflib.pc.
 2020-08-27 18:18:55 +03:00
Efraim Flashner
6d8dd5bad7
gnu: vcflib: Use shared libraries. 
* gnu/packages/bioinformatics.scm (vcflib)[source]: Add patch. Add
snippet to adjust files for new locations.
[inputs]: Add fastahack, smithwaterman, tabixpp, xz.
[native-inputs]: Add pkg-config. Remove the package-source of fastahack,
fsom, smithwaterman, tabixpp.
[arguments]: Remove make-flags. Add custom phase to add the output lib
directory to the rpath. Adjust custom 'unpack-submodule-sources for the
change in native-inputs. Adjust custom 'install phase to also install
libraries and headers.
* gnu/packages/patches/vcflib-use-shared-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2020-08-27 18:18:55 +03:00
Efraim Flashner
4bbcbe93cd
gnu: fastahack: Install pkgconfig file. 
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Adjust custom
'install phase to add fastahack.pc.
 2020-08-27 18:09:28 +03:00
Efraim Flashner
f075bf09bd
gnu: fastahack: Build and install shared library and headers. 
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Add phase to
build PIE objects. Add custom phase to build dynamic library. Adjust
custom 'install phase to install shared library and headers.
 2020-08-27 18:08:13 +03:00
Efraim Flashner
5c78997188
gnu: smithwaterman: Install pkgconfig file. 
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Adjust
custom 'install phase to add smithwaterman.pc file.
 2020-08-27 18:06:25 +03:00
Efraim Flashner
afa352223f
gnu: smithwaterman: Build and install shared library and headers. 
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add custom
phase to build PIE objects. Add custom 'build-dynamic phase to build
dynamic library. Adjust custom 'install phase to install shared library
and headers.
 2020-08-27 18:05:20 +03:00
Efraim Flashner
261bc778b6
gnu: tabixpp: Install pkgconfig file. 
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom
'install phase to add tabixpp.pc file.
 2020-08-27 18:03:13 +03:00
Efraim Flashner
35cb1bc527
gnu: tabixpp: Build and install shared library and headers. 
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom
'build phase to build shared library. Adjust custom 'install phase to
install libraries and header.
 2020-08-27 18:02:16 +03:00
Ricardo Wurmus
4e0acfe5e7
gnu: r-complexheatmap: Update to 2.4.3. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.3.
 2020-08-20 21:25:34 +02:00
Ricardo Wurmus
e9d2cab0bf
gnu: r-gage: Update to 2.38.3. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.38.3.
[propagated-inputs]: Add r-go-db.
 2020-08-20 21:25:34 +02:00
Ricardo Wurmus
9da4a25b33
gnu: r-annotationhub: Update to 2.20.2. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.2.
 2020-08-20 21:25:34 +02:00
Ricardo Wurmus
67f8477fb5
gnu: r-delayedarray: Update to 0.14.1. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.1.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
b414add3d1
gnu: r-annotationdbi: Update to 1.50.3. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.3.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
e9128480d4
gnu: r-biocviews: Update to 1.56.2. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.2.
 2020-08-20 21:25:33 +02:00
Ricardo Wurmus
6e5be7ffad
gnu: pigx-chipseq: Update to 0.0.43. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.43.
 2020-08-19 12:12:42 +02:00
Ricardo Wurmus
346ea4b5fc
gnu: bowtie1: Add missing Python input. 
Reported-by: Marcel Schilling <marcel.schilling@mdc-berlin.de>

* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Add python-wrapper.
 2020-08-18 12:38:38 +02:00
Ricardo Wurmus
4d55432fd0
gnu: pigx-bsseq: Update to 0.1.2. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.2.
[inputs]: Add r-ggrepel, bwa-meth, methyldackel, multiqc, and samblaster.
 2020-08-16 15:57:27 +02:00
Ricardo Wurmus
6f5530b9bc
gnu: pigx-scrnaseq: Use statically linked Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
 2020-08-16 15:57:27 +02:00
Ricardo Wurmus
ac6eba4eb4
gnu: pigx-bsseq: Use statically linked Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
 2020-08-16 15:57:27 +02:00
Ricardo Wurmus
c0ad6dc976
gnu: pigx-chipseq: Use statically linked Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
 2020-08-16 15:57:27 +02:00
Ricardo Wurmus
2cb9f0f2a6
gnu: pigx-rnaseq: Use statically linked Pandoc. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
 2020-08-16 15:57:27 +02:00
Ricardo Wurmus
19afa4d58f
gnu: r-rcas: Use pandoc instead of ghc-pandoc. 
* gnu/packages/bioinformatics.scm (r-rcas)[propagated-inputs]: Replace
ghc-pandoc with pandoc.
 2020-08-16 15:57:25 +02:00
Ricardo Wurmus
e6bdc6949b
gnu: hisat2: Use pandoc instead of ghc-pandoc. 
* gnu/packages/bioinformatics.scm (hisat2)[native-inputs]: Replace ghc-pandoc
with pandoc.
 2020-08-15 10:10:39 +02:00
Ricardo Wurmus
bcdc61bfa1
gnu: tophat: Hide default GCC. 
* gnu/packages/bioinformatics.scm (tophat)[arguments]: Add build phase
"hide-default-gcc".
 2020-08-12 21:55:06 +02:00
Ricardo Wurmus
8ca7141c02
gnu: r-seurat: Update to 3.2.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.2.0.
[propagated-inputs]: Remove r-tsne; add r-jsonlite, r-miniui, r-shiny, r-spatstat, and r-tibble.
 2020-08-12 13:57:10 +02:00
Ricardo Wurmus
a62aadf216
gnu: Add phast. 
* gnu/packages/bioinformatics.scm (phast): New variable.
 2020-08-10 21:58:38 +02:00
Ricardo Wurmus
92b34df789
gnu: clipper: Update to 2.0. 
* gnu/packages/bioinformatics.scm (clipper): Update to 2.0.
[source]: Remove snippet.
[arguments]: Build with Python 3; remove phase "fix-typo", add phase
"make-files-writable".
[inputs]: Replace all Python 2 variants with Python 3 variants.
[native-inputs]: Add python-setuptools-git.
 2020-08-07 12:53:23 +02:00
Jakub Kądziołka
6a7bdbfa2d
gnu: paml: Fix build. 
* gnu/packages/bioinformatics.scm (paml)[snippet]: Fix permissions
  before repacking the source tarball.
 2020-07-30 03:48:50 +02:00
Marius Bakke
e1409c764f
gnu: check: Update to 0.15.1. 
* gnu/packages/check.scm (check): Update to 0.15.1.
(check-0.14): New public variable.
* gnu/packages/backup.scm (burp)[native-inputs]: Change from CHECK to
CHECK-0.14.
* gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Likewise.
* gnu/packages/databases.scm (recutils)[native-inputs]: Likewise.
* gnu/packages/electronics.scm (libsigrokdecode)[native-inputs]: Likewise.
* gnu/packages/enlightenment.scm (efl, edi)[native-inputs]: Likewise.
* gnu/packages/gnome.scm (gdm)[inputs]: Likewise.
* gnu/packages/gtk.scm (girara)[native-inputs]: Likewise.
* gnu/packages/messaging.scm (pidgin)[native-inputs]: Likewise.
* gnu/packages/networking.scm (iodine)[native-inputs]: Likewise.
* gnu/packages/pulseaudio.scm (pulseaudio)[native-inputs]: Likewise.
* gnu/packages/sssd.scm (sssd)[native-inputs]: Likewise.
* gnu/packages/web.scm (libwapcaplet)[native-inputs]: Likewise.
 2020-07-25 16:16:11 +02:00
Jakub Kądziołka
56f12a65a0
gnu: r-rhdf5lib: Fix libsz substitution. 
This is a follow-up to commit b7f051db14 -
in the new version, some of the format strings being replaced gained
quotes. This commit fixes build of dependents of r-rhdf5lib, such as
r-hdf5array.

* gnu/packages/bioinformatics (r-rhdf5lib): Remove all instances of libsz.a.
 2020-07-19 15:54:48 +02:00
Tobias Geerinckx-Rice
fe39c70195
gnu: Use HTTPS for mdc-berlin.de home pages. 
* gnu/packages/bioinformatics.scm (r-genomation, r-genomationdata, pigx-rnaseq)
(pigx-chipseq, pigx-bsseq, pigx-scrnaseq, pigx)[home-page]: Use HTTPS.
 2020-07-16 20:12:06 +02:00
Tobias Geerinckx-Rice
c980589260
gnu: Use HTTPS for biojava.org home pages. 
* gnu/packages/bioinformatics.scm (java-biojava-core)
(java-biojava-phylo, java-biojava-alignment, java-biojava-phylo-4.0)
(java-biojava-alignment-4.0)[home-page]: Use HTTPS.
 2020-07-16 20:12:06 +02:00
Ricardo Wurmus
b7f051db14
gnu: r-rhdf5lib: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.1.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus
82eafe32a2
gnu: r-qtl2: Update to 0.22-11. 
* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-11.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus
16e16586d2
gnu: r-genomicfeatures: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.1.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus
02f3a622e2
gnu: r-summarizedexperiment: Update to 1.18.2. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.2.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus
b80f141f86
gnu: r-delayedmatrixstats: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.1.
 2020-07-16 10:08:03 +02:00
Ricardo Wurmus
15597255e6
gnu: r-rhdf5: Update to 2.32.2. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.2.
 2020-07-16 10:08:03 +02:00
Ludovic Courtès
b0e7b6992f
gnu: Remove ".git" from "https://github/…/….git". 
Until now, 'lookup-origin' and thus 'lookup-origin-revision' in (guix
swh) would sometimes return #f for these because the ".git" URLs are
redirects to the non-".git" URLs.  Consequently, 'guix lint -c archival'
would keep saying "scheduled Software Heritage archival"; likewise, the
fallback download code would fail.

* gnu/packages/ada.scm,
gnu/packages/admin.scm,
gnu/packages/aidc.scm,
gnu/packages/algebra.scm,
gnu/packages/android.scm,
gnu/packages/animation.scm,
gnu/packages/arcan.scm,
gnu/packages/assembly.scm,
gnu/packages/audio.scm,
gnu/packages/authentication.scm,
gnu/packages/avr.scm,
gnu/packages/axoloti.scm,
gnu/packages/backup.scm,
gnu/packages/bash.scm,
gnu/packages/benchmark.scm,
gnu/packages/bioconductor.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/bittorrent.scm,
gnu/packages/boost.scm,
gnu/packages/build-tools.scm,
gnu/packages/c.scm,
gnu/packages/calendar.scm,
gnu/packages/cdrom.scm,
gnu/packages/check.scm,
gnu/packages/chemistry.scm,
gnu/packages/chez.scm,
gnu/packages/clojure.scm,
gnu/packages/code.scm,
gnu/packages/compression.scm,
gnu/packages/compton.scm,
gnu/packages/coq.scm,
gnu/packages/cpp.scm,
gnu/packages/cran.scm,
gnu/packages/crypto.scm,
gnu/packages/curl.scm,
gnu/packages/databases.scm,
gnu/packages/datastructures.scm,
gnu/packages/debug.scm,
gnu/packages/disk.scm,
gnu/packages/distributed.scm,
gnu/packages/django.scm,
gnu/packages/dlang.scm,
gnu/packages/dns.scm,
gnu/packages/docker.scm,
gnu/packages/education.scm,
gnu/packages/efi.scm,
gnu/packages/elixir.scm,
gnu/packages/emacs-xyz.scm,
gnu/packages/embedded.scm,
gnu/packages/emulators.scm,
gnu/packages/engineering.scm,
gnu/packages/erlang.scm,
gnu/packages/fabric-management.scm,
gnu/packages/file-systems.scm,
gnu/packages/finance.scm,
gnu/packages/firmware.scm,
gnu/packages/flashing-tools.scm,
gnu/packages/fonts.scm,
gnu/packages/fontutils.scm,
gnu/packages/fpga.scm,
gnu/packages/game-development.scm,
gnu/packages/games.scm,
gnu/packages/genealogy.scm,
gnu/packages/genimage.scm,
gnu/packages/geo.scm,
gnu/packages/gimp.scm,
gnu/packages/gl.scm,
gnu/packages/gnome-xyz.scm,
gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm,
gnu/packages/golang.scm,
gnu/packages/gpodder.scm,
gnu/packages/graph.scm,
gnu/packages/graphics.scm,
gnu/packages/graphviz.scm,
gnu/packages/groff.scm,
gnu/packages/groovy.scm,
gnu/packages/gtk.scm,
gnu/packages/guile-xyz.scm,
gnu/packages/guile.scm,
gnu/packages/hardware.scm,
gnu/packages/haskell-apps.scm,
gnu/packages/haskell-xyz.scm,
gnu/packages/hexedit.scm,
gnu/packages/i2p.scm,
gnu/packages/ibus.scm,
gnu/packages/image-processing.scm,
gnu/packages/image-viewers.scm,
gnu/packages/image.scm,
gnu/packages/ipfs.scm,
gnu/packages/java-graphics.scm,
gnu/packages/java-maths.scm,
gnu/packages/java.scm,
gnu/packages/javascript.scm,
gnu/packages/jrnl.scm,
gnu/packages/julia.scm,
gnu/packages/jupyter.scm,
gnu/packages/kodi.scm,
gnu/packages/language.scm,
gnu/packages/lego.scm,
gnu/packages/less.scm,
gnu/packages/libusb.scm,
gnu/packages/linux.scm,
gnu/packages/lirc.scm,
gnu/packages/lisp-xyz.scm,
gnu/packages/llvm.scm,
gnu/packages/logging.scm,
gnu/packages/lolcode.scm,
gnu/packages/lua.scm,
gnu/packages/lxde.scm,
gnu/packages/lxqt.scm,
gnu/packages/machine-learning.scm,
gnu/packages/mail.scm,
gnu/packages/markup.scm,
gnu/packages/maths.scm,
gnu/packages/maven.scm,
gnu/packages/mes.scm,
gnu/packages/messaging.scm,
gnu/packages/monitoring.scm,
gnu/packages/mpd.scm,
gnu/packages/music.scm,
gnu/packages/networking.scm,
gnu/packages/node-xyz.scm,
gnu/packages/ocaml.scm,
gnu/packages/ocr.scm,
gnu/packages/onc-rpc.scm,
gnu/packages/opencl.scm,
gnu/packages/opencog.scm,
gnu/packages/pantheon.scm,
gnu/packages/password-utils.scm,
gnu/packages/patchutils.scm,
gnu/packages/pdf.scm,
gnu/packages/perl6.scm,
gnu/packages/phabricator.scm,
gnu/packages/popt.scm,
gnu/packages/printers.scm,
gnu/packages/prolog.scm,
gnu/packages/protobuf.scm,
gnu/packages/pulseaudio.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/python-xyz.scm,
gnu/packages/qt.scm,
gnu/packages/radio.scm,
gnu/packages/rails.scm,
gnu/packages/rdf.scm,
gnu/packages/rednotebook.scm,
gnu/packages/rpc.scm,
gnu/packages/rsync.scm,
gnu/packages/ruby.scm,
gnu/packages/rust.scm,
gnu/packages/scheme.scm,
gnu/packages/screen.scm,
gnu/packages/security-token.scm,
gnu/packages/selinux.scm,
gnu/packages/serialization.scm,
gnu/packages/shells.scm,
gnu/packages/shellutils.scm,
gnu/packages/simh.scm,
gnu/packages/sml.scm,
gnu/packages/ssh.scm,
gnu/packages/statistics.scm,
gnu/packages/stenography.scm,
gnu/packages/sync.scm,
gnu/packages/syncthing.scm,
gnu/packages/synergy.scm,
gnu/packages/telephony.scm,
gnu/packages/terminals.scm,
gnu/packages/tex.scm,
gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm,
gnu/packages/textutils.scm,
gnu/packages/time.scm,
gnu/packages/tmux.scm,
gnu/packages/tor.scm,
gnu/packages/toys.scm,
gnu/packages/version-control.scm,
gnu/packages/video.scm,
gnu/packages/vim.scm,
gnu/packages/virtualization.scm,
gnu/packages/vlang.scm,
gnu/packages/vnc.scm,
gnu/packages/vpn.scm,
gnu/packages/web-browsers.scm,
gnu/packages/web.scm,
gnu/packages/wireservice.scm,
gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm,
gnu/packages/xdisorg.scm,
gnu/packages/xml.scm,
gnu/packages/xorg.scm,
tests/lint.scm: Remove trailing ".git" from 'git-reference' URL.
 2020-07-12 23:08:15 +02:00
Ricardo Wurmus
bd978be3ae
gnu: r-annotationdbi: Update to 1.50.1. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.1.
 2020-07-02 12:45:53 +02:00