zimoun
d5576b6eb7
gnu: r-grohmm: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-grohmm): Move from here...
* gnu/packages/bioconductor.scm (r-grohmm): ...to here.
2021-03-15 14:04:26 +01:00
zimoun
5ac55aea8b
gnu: r-biocstyle: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Move from here...
* gnu/packages/bioconductor.scm (r-biocstyle): ...to here.
2021-03-15 14:03:21 +01:00
zimoun
134404b437
gnu: r-biocviews: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-biocviews): Move from here...
* gnu/packages/bioconductor.scm (r-biocviews): ...to here.
2021-03-15 14:03:18 +01:00
Ricardo Wurmus
6e0ed09e68
gnu: Add instrain.
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* gnu/packages/bioinformatics.scm (instrain): New variable.
2021-03-15 11:43:20 +01:00
Ricardo Wurmus
ad34eb222c
gnu: Add python-drep.
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* gnu/packages/bioinformatics.scm (python-drep): New variable.
2021-03-15 11:43:20 +01:00
zimoun
df6b3c25bb
gnu: r-systempiper: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-systempiper): Move from here...
* gnu/packages/bioconductor.scm (r-systempiper): ...to here.
2021-03-12 14:45:55 +01:00
zimoun
8957efa8ef
gnu: r-shortread: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
2021-03-12 14:45:54 +01:00
zimoun
2a97057688
gnu: r-gostats: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-gostats): Move from here...
* gnu/packages/bioconductor.scm (r-gostats): ...to here.
2021-03-12 14:45:54 +01:00
zimoun
4e7cf96c9f
gnu: r-category: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-category): Move from here...
* gnu/packages/bioconductor.scm (r-category): ...to here.
2021-03-12 14:45:54 +01:00
zimoun
031fdda47a
gnu: r-gseabase: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gseabase): Move from here...
* gnu/packages/bioconductor.scm (r-gseabase): ...to here.
2021-03-12 14:45:54 +01:00
zimoun
f44079bc21
gnu: r-rbgl: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-rbgl): Move from here...
* gnu/packages/bioconductor.scm (r-rbgl): ...to here.
2021-03-12 14:45:54 +01:00
zimoun
ff92c2873c
gnu: r-annotationforge: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Move from here...
* gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
2021-03-12 14:45:53 +01:00
zimoun
d769b10714
gnu: r-dexseq: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-dexseq): Move from here...
* gnu/packages/bioconductor.scm (r-dexseq): ...to here.
2021-03-12 14:45:53 +01:00
zimoun
373545855d
gnu: r-deseq2: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-deseq2): Move from here...
* gnu/packages/bioconductor.scm (r-deseq2): ...to here.
2021-03-12 14:45:53 +01:00
zimoun
a35ea5fed9
gnu: r-genefilter: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-genefilter): Move from here...
* gnu/packages/bioconductor.scm (r-genefilter): ...to here.
2021-03-12 14:45:53 +01:00
Efraim Flashner
5ae7414860
gnu: Add bandage.
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* gnu/packages/bioinformatics.scm (bandage): New variable.
2021-03-11 16:54:38 +02:00
Ricardo Wurmus
133a918923
gnu: trim-galore: Update to 0.6.6.
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* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.6.
2021-03-09 11:54:59 +01:00
Ricardo Wurmus
49d85b3f11
gnu: bbmap: Update to 38.90.
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* gnu/packages/bioinformatics.scm (bbmap): Update to 38.90.
2021-03-09 11:54:59 +01:00
Nicolas Goaziou
ea8e89292c
gnu: seqan-1: Use HTTPS source URI.
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* gnu/packages/bioinformatics.scm (seqan-1)[source]: Use HTTPS URI.
2021-03-06 16:05:44 +01:00
Nicolas Goaziou
e062572812
gnu: seqan: Use HTTPS home page URI.
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* gnu/packages/bioinformatics.scm (seqan)[home-page]: Use HTTPS URI.
2021-03-06 16:01:24 +01:00
Ricardo Wurmus
f5c3e8e2ec
gnu: Add r-cellchat.
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* gnu/packages/bioinformatics.scm (r-cellchat): New variable.
2021-03-05 15:04:15 +01:00
Tim Howes
dcee10506c
gnu: infernal: Update to 1.1.4.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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
2021-02-23 19:40:59 +01:00
Ricardo Wurmus
f1f6e49190
gnu: star: Update to 2.7.8a.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (prinseq): New variable.
2021-02-19 23:14:59 +01:00
Ricardo Wurmus
80d3150c94
gnu: Add ngshmmalign.
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* gnu/packages/bioinformatics.scm (ngshmmalign): New variable.
2021-02-19 17:24:52 +01:00
Ricardo Wurmus
8360705948
gnu: Add r-archr.
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* gnu/packages/bioinformatics.scm (r-archr): New variable.
2021-02-18 16:11:38 +01:00
Ricardo Wurmus
9904a15a4c
gnu: Add indelfixer.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (r-demultiplex): New variable.
2021-01-28 22:24:51 +01:00
Ricardo Wurmus
04b1a1f6bd
gnu: Add repeat-masker.
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* gnu/packages/bioinformatics.scm (repeat-masker): New variable.
2021-01-28 15:07:55 +01:00
