8f1237c350
gnu: r-ldblock: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-ldblock): Move from here...
* gnu/packages/bioconductor.scm (r-ldblock): ...to here.
2020-12-29 17:40:28 +01:00
9534e7b706
gnu: r-gqtlstats: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
2020-12-29 17:40:28 +01:00
2a4322f7c3
gnu: r-gviz: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gviz): Move from here...
* gnu/packages/bioconductor.scm (r-gviz): ...to here.
2020-12-29 17:40:28 +01:00
69a5e066c1
gnu: r-gwascat: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gwascat): Move from here...
* gnu/packages/bioconductor.scm (r-gwascat): ...to here.
2020-12-29 17:40:28 +01:00
838db0de5e
gnu: r-sushi: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-sushi): Move from here...
* gnu/packages/bioconductor.scm (r-sushi): ...to here.
2020-12-29 17:40:25 +01:00
6203b8e5bd
gnu: kentutils: Build with OpenSSL 1.1.
...
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL-1.0
to OPENSSL.
2020-12-20 16:30:42 +01:00
ca27b0e528
gnu: kentutils: Add a file name for the "samtabix" input.
...
* gnu/packages/bioinformatics.scm (kentutils)[native-inputs]: For "samtabix",
add a file name on the origin.
2020-12-20 16:30:42 +01:00
48f77ecbb1
gnu: r-keggrest: Update to 1.30.1.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.1.
2020-12-09 23:30:12 +01:00
4745f0dfca
gnu: r-genomeinfodb: Update to 1.26.2.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.2.
2020-12-09 23:30:12 +01:00
baeaa02e75
gnu: r-biocstyle: Update to 2.18.1.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.1.
2020-12-09 23:30:12 +01:00
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
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
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
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
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
86fcceeae1
gnu: Add r-rhdf5filters.
...
* gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable.
2020-12-09 12:12:46 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
bff94a5a53
Merge branch 'master' into staging
2020-11-26 01:08:35 +01:00
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
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
87a027243f
Merge branch 'master' into staging
2020-11-23 23:39:47 +01:00
964bc9e5fe
gnu: Add cwltool.
...
* gnu/packages/bioinformatics.scm (cwltool): New variable.
2020-11-23 15:43:38 +02:00
7face25953
gnu: Add python-schema-salad.
...
* gnu/packages/bioinformatics.scm (python-schema-salad): New variable.
2020-11-23 15:43:37 +02:00
4e5e05d409
Merge branch 'master' into staging
2020-11-15 23:45:34 +01:00
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
37ba374a53
gnu: Fix build for python-pysam.
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* 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
ecc309c142
gnu: Add bcftools-1.9.
...
* gnu/packages/bioinformatics.scm (bcftools-1.9): New variable.
2020-11-13 16:14:01 +01:00
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
da4a38edad
gnu: Add samtools-1.9.
...
* gnu/packages/bioinformatics.scm (samtools-1.9): New variable.
2020-11-13 14:49:27 +01:00
3ede804f6d
gnu: Add htslib-1.9.
...
* gnu/packages/bioinformatics.scm (htslib-1.9): New variable.
2020-11-13 14:49:20 +01:00
a9a0d34874
Merge branch 'master' into staging
2020-11-11 00:02:32 +01:00
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
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
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
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
bcbd536e3f
gnu: Update samtools to 1.11.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.11.
2020-10-29 16:55:07 +01:00
04a49b4143
gnu: Update bcftools to 1.11.
...
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.11.
2020-10-29 16:55:03 +01:00
f40add4dbb
gnu: Update htslib to 1.11.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.11.
2020-10-29 16:54:55 +01:00
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
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
f7175626ff
Merge branch 'master' into staging
2020-10-13 23:39:27 +02:00
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
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
906c79d1a3
gnu: r-rhdf5: Update to 2.32.3.
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* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.3.
2020-10-06 13:23:38 +02:00
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
87c079d9b5
Merge branch 'master' into staging
2020-10-05 14:17:25 +02:00
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
2374443561
Merge branch 'staging' into wip-lisp
2020-09-23 14:50:19 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Marius Bakke
Ricardo Wurmus
Roel Janssen
Efraim Flashner
Maxim Cournoyer
Ludovic Courtès
Guillaume Le Vaillant
Mădălin Ionel Patrașcu
Nicolas Goaziou