Ricardo Wurmus
|
c2b45ac578
|
gnu: r-diversitree: Update to 0.9-11.
* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-11.
|
2019-03-21 00:02:49 +01:00 |
|
Ricardo Wurmus
|
db39269c89
|
gnu: r-maldiquant: Update to 1.19.2.
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.2.
|
2019-03-21 00:02:49 +01:00 |
|
Ricardo Wurmus
|
28d0eb2565
|
gnu: r-diversitree: Fix typo.
* gnu/packages/bioinformatics.scm (r-diversitree)[propagated-inputs]: Fix typo
in package labels.
|
2019-03-21 00:02:48 +01:00 |
|
Ricardo Wurmus
|
933cc19684
|
gnu: r-annotationhub: Update to 2.14.5.
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.5.
|
2019-03-20 22:32:37 +01:00 |
|
Ricardo Wurmus
|
e49d5d34ed
|
gnu: r-genomicfeatures: Update to 1.34.6.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.6.
|
2019-03-20 22:32:32 +01:00 |
|
Ricardo Wurmus
|
2b83d218d8
|
gnu: r-variantannotation: Update to 1.28.13.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.13.
|
2019-03-20 22:32:25 +01:00 |
|
Ricardo Wurmus
|
0adb6f207b
|
gnu: r-category: Update to 2.48.1.
* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.1.
|
2019-03-20 22:32:17 +01:00 |
|
Ricardo Wurmus
|
e014dc78f0
|
gnu: r-dexseq: Update to 1.28.3.
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.3.
|
2019-03-20 22:32:11 +01:00 |
|
Ricardo Wurmus
|
35f9c6628f
|
gnu: Add adapterremoval.
* gnu/packages/bioinformatics.scm (adapterremoval): New variable.
|
2019-03-20 12:19:55 +01:00 |
|
Ricardo Wurmus
|
c5542196d5
|
gnu: nanopolish: Use python-wrapper.
* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Replace "python" with
"python-wrapper" as scripts require "python" executable.
|
2019-03-19 13:30:41 +01:00 |
|
Ricardo Wurmus
|
7c1685e9d8
|
gnu: nanopolish: Remove bundled library sources.
* gnu/packages/bioinformatics.scm (nanopolish)[source]: Add snippet to remove
bundled htslib sources.
|
2019-03-19 13:30:41 +01:00 |
|
Ricardo Wurmus
|
9e1d9a0a46
|
gnu: python-biom-format: Fix build.
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Remove
generated C files.
[arguments]: Disable second broken test.
|
2019-03-18 23:46:27 +01:00 |
|
Ricardo Wurmus
|
6e42cef0ab
|
gnu: Add bbmap.
* gnu/packages/bioinformatics.scm (bbmap): New variable.
|
2019-03-18 21:35:57 +01:00 |
|
Ricardo Wurmus
|
ee4ca57809
|
gnu: blasr: Add home page.
Reported by Efraim Flashner <efraim@flashner.co.il> on IRC.
* gnu/packages/bioinformatics.scm (blasr)[home-page]: Add it.
|
2019-03-18 16:02:30 +01:00 |
|
Ricardo Wurmus
|
19bd7f2e79
|
gnu: Add arriba.
* gnu/packages/bioinformatics.scm (arriba): New variable.
|
2019-03-18 16:00:30 +01:00 |
|
Ricardo Wurmus
|
f88bdc5ff9
|
gnu: Add blasr.
* gnu/packages/bioinformatics.scm (blasr): New variable.
|
2019-03-18 14:47:49 +01:00 |
|
Ricardo Wurmus
|
6a6cd48cf0
|
gnu: Add blasr-libcpp.
* gnu/packages/bioinformatics.scm (blasr-libcpp): New variable.
|
2019-03-18 14:47:45 +01:00 |
|
Ricardo Wurmus
|
55154c5f40
|
gnu: Add pbbam.
* gnu/packages/bioinformatics.scm (pbbam): New variable.
|
2019-03-18 14:47:26 +01:00 |
|
Ricardo Wurmus
|
07c8b558e3
|
gnu: Add bwa-meth.
* gnu/packages/bioinformatics.scm (bwa-meth): New variable.
|
2019-03-15 11:36:56 +01:00 |
|
Ricardo Wurmus
|
fd4c7a098a
|
gnu: Add python-velocyto.
* gnu/packages/bioinformatics.scm (python-velocyto): New variable.
|
2019-03-13 22:48:53 +01:00 |
|
Ricardo Wurmus
|
55a0a3c853
|
gnu: python-loompy: Update to 2.0.17.
* gnu/packages/bioinformatics.scm (python-loompy): Update to 2.0.17.
[source]: Fetch via git.
[arguments]: Enable tests, replace "check" phase.
[propagated-inputs]: Add python-pandas.
[native-inputs]: Add python-pytest.
|
2019-03-13 22:48:52 +01:00 |
|
Ricardo Wurmus
|
0b5d12ccdf
|
gnu: Add tetoolkit.
* gnu/packages/bioinformatics.scm (tetoolkit): New variable.
|
2019-03-13 15:14:10 +01:00 |
|
Ricardo Wurmus
|
4dc2ecc279
|
gnu: r-qvalue: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-qvalue): Move from here...
* gnu/packages/bioconductor.scm (r-qvalue): ...to here.
|
2019-03-12 22:47:56 +01:00 |
|
Ricardo Wurmus
|
8b6acb1f20
|
gnu: blast+: Update to 2.7.1.
* gnu/packages/bioinformatics.scm (blast+): Update to 2.7.1.
[inputs]: Add lmdb.
[source]: Remove obsolete patch.
* gnu/package/patches/blast+-fix-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
|
2019-03-08 23:00:07 +01:00 |
|
Ricardo Wurmus
|
183b6575e7
|
gnu: r-mzr: Update to 2.16.2.
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.2.
[inputs]: Replace "boost" with "boost-for-mysql".
|
2019-03-08 09:14:01 +01:00 |
|
Ricardo Wurmus
|
6453d7aecc
|
gnu: r-gviz: Update to 1.26.5.
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.5.
|
2019-03-08 09:14:01 +01:00 |
|
Ricardo Wurmus
|
101dcc29d3
|
gnu: r-ensembldb: Update to 2.6.7.
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.7.
|
2019-03-08 09:14:01 +01:00 |
|
Ricardo Wurmus
|
d3713237c5
|
gnu: r-annotationhub: Update to 2.14.4.
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.4.
|
2019-03-08 09:14:01 +01:00 |
|
Ricardo Wurmus
|
53e7f028ed
|
gnu: r-rhtslib: Update to 1.14.1.
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.1.
|
2019-03-08 09:14:01 +01:00 |
|
Ricardo Wurmus
|
d86b9eca56
|
gnu: r-genomicfeatures: Update to 1.34.4.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.4.
|
2019-03-08 09:14:01 +01:00 |
|
Ricardo Wurmus
|
d493043daf
|
gnu: r-rtracklayer: Update to 1.42.2.
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.2.
|
2019-03-08 09:14:01 +01:00 |
|
Ricardo Wurmus
|
57f40dc220
|
gnu: r-rsamtools: Update to 1.34.1.
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.1.
|
2019-03-08 09:14:00 +01:00 |
|
Ricardo Wurmus
|
58209b1e21
|
gnu: r-biocparallel: Update to 1.16.6.
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.6.
|
2019-03-08 09:14:00 +01:00 |
|
Ricardo Wurmus
|
cd43ae3fd6
|
gnu: r-variantannotation: Update to 1.28.11.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.11.
|
2019-03-08 09:14:00 +01:00 |
|
Ricardo Wurmus
|
fff11bccc6
|
gnu: r-genomeinfodb: Update to 1.18.2.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.2.
|
2019-03-08 09:14:00 +01:00 |
|
Ricardo Wurmus
|
8972989e10
|
gnu: r-dexseq: Update to 1.28.2.
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.2.
|
2019-03-08 09:14:00 +01:00 |
|
Ricardo Wurmus
|
3b296475bf
|
gnu: cd-hit: Support longer sequences.
* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Pass MAX_SEQ to make
flags.
|
2019-03-07 13:38:01 +01:00 |
|
Ricardo Wurmus
|
8035819f4c
|
gnu: r-org-mm-eg-db: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Move from here...
* gnu/packages/bioconductor.scm (r-org-mm-eg-db): ...to here.
|
2019-03-06 21:43:33 +01:00 |
|
Ricardo Wurmus
|
d56df35a25
|
gnu: r-org-hs-eg-db: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Move from here...
* gnu/packages/bioconductor.scm (r-org-hs-eg-db): ...to here.
|
2019-03-06 21:42:39 +01:00 |
|
Ricardo Wurmus
|
f8780e96ff
|
gnu: r-org-dm-eg-db: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Move from here...
* gnu/packages/bioconductor.scm (r-org-dm-eg-db): ...to here.
|
2019-03-06 21:41:48 +01:00 |
|
Ricardo Wurmus
|
3a08940e1a
|
gnu: r-org-ce-eg-db: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Move from here...
* gnu/packages/bioconductor.scm (r-org-ce-eg-db): ...to here.
|
2019-03-06 21:35:20 +01:00 |
|
Ricardo Wurmus
|
7bc5d1b0e1
|
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Move from here...
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
...to here.
|
2019-03-06 21:33:17 +01:00 |
|
Ricardo Wurmus
|
13dabd6947
|
gnu: r-bsgenome-dmelanogaster-ucsc-dm3: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3):
...to here.
|
2019-03-06 21:31:41 +01:00 |
|
Ricardo Wurmus
|
0c792ffbd1
|
gnu: r-bsgenome-celegans-ucsc-ce10: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce10): ...to here.
|
2019-03-06 21:30:30 +01:00 |
|
Ricardo Wurmus
|
b7d93cf508
|
gnu: r-bsgenome-celegans-ucsc-ce6: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce6): ...to here.
|
2019-03-06 21:29:20 +01:00 |
|
Ricardo Wurmus
|
c3adc83054
|
gnu: r-bsgenome-mmusculus-ucsc-mm10: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm10): ...to here.
|
2019-03-06 21:26:54 +01:00 |
|
Ricardo Wurmus
|
5acb9052cf
|
gnu: r-bsgenome-mmusculus-ucsc-mm9: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9): ...to here.
|
2019-03-06 21:25:18 +01:00 |
|
Ricardo Wurmus
|
fe0b76e215
|
gnu: r-bsgenome-hsapiens-ucsc-hg19: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): ...to here.
|
2019-03-06 21:23:42 +01:00 |
|
Ricardo Wurmus
|
40a6505711
|
gnu: r-bsgenome-hsapiens-1000genomes-hs37d5: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
...to here.
|
2019-03-06 21:23:20 +01:00 |
|
Ricardo Wurmus
|
66e35ce63b
|
gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): Move
from here...
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): ...to
here.
|
2019-03-06 21:16:33 +01:00 |