aeca5f0c5b
gnu: r-scran: Update to 1.6.9.
...
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.9.
2018-04-21 23:07:52 +02:00
80323c3c13
gnu: r-hitc: Update to 1.22.1.
...
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.22.1.
2018-04-21 23:07:52 +02:00
b6d7deca55
gnu: r-ldblock: Update to 1.8.1.
...
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.8.1.
2018-04-21 23:07:52 +02:00
fb1dcfac46
gnu: r-erma: Update to 0.10.1.
...
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.10.1.
2018-04-21 23:07:52 +02:00
8defca1d94
gnu: r-gprofiler: Update to 0.6.6.
...
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.6.
2018-04-21 23:07:52 +02:00
fc6d3e2606
gnu: r-ggbio: Update to 1.26.1.
...
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.26.1.
2018-04-21 23:07:52 +02:00
0bd5c7b859
gnu: r-genomicalignments: Update to 1.14.2.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.2.
2018-04-21 23:07:52 +02:00
4207770218
gnu: r-dexseq: Update to 1.24.4.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.4.
2018-04-21 23:07:52 +02:00
3db5d04ccc
gnu: r-vegan: Update to 2.5-1.
...
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-1.
[propagated-inputs]: Add r-knitr.
2018-04-21 23:07:52 +02:00
482959ffa4
gnu: sambamba: Update to 0.6.7-10-g223fa20.
...
* gnu/packages/bioinformatics.scm (sambamba)[source]: Fetch from git.
[arguments]: Disable parallel build; rename build phase "place-biod" to
"place-biod-and-undead"; add build phase "fix-ldc-version"; adjust phase
"unbundle-prerequisites".
[native-inputs]: Add python2-minimal; update biod sources; add undead sources.
2018-04-06 17:12:15 +02:00
262ee8eae2
gnu: htslib-for-sambamba: Fix build.
...
* gnu/packages/bioinformatics.scm (htslib-for-sambamba)[arguments]: Do not
inherit htslib arguments.
2018-04-06 17:12:07 +02:00
fdc306879b
gnu: Add delly.
...
* gnu/packages/bioinformatics.scm (delly): New variable.
* gnu/packages/patches/delly-use-system-libraries.patch: New file.
* gnu/local.mk: Include delly-use-system-libraries.patch.
Signed-off-by: Leo Famulari <leo@famulari.name>
2018-03-30 10:48:01 -04:00
f38ac742e6
gnu: mash: Update to 2.0.
...
* gnu/packages/bioinformatics.scm (mash): Update to 2.0.
2018-03-30 12:18:35 +10:00
c7a8aa131d
gnu: mafft: Update to 7.394.
...
* gnu/packages/bioinformatics.scm (mafft): Update to 7.394.
2018-03-30 12:18:35 +10:00
9a40b8d9b2
gnu: diamond: Update to 0.9.19.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19.
2018-03-30 12:18:35 +10:00
e086d2f68b
gnu: r-mutationalpatterns: Update to 1.4.3.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3;
[propagated-inputs]: Remove r-gridextra.
2018-03-29 15:50:44 +02:00
53e42694e5
gnu: kaiju: Update to 1.6.2.
...
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2;
[inputs]: Add zlib.
2018-03-29 15:40:52 +02:00
904c3a4e99
gnu: r-annotate: Update to 1.56.2.
...
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.2.
2018-03-25 00:36:31 +01:00
618050a126
gnu: r-bookdown: Do not propagate ghc-pandoc.
...
This package propagates r-rmarkdown, which propagates its own variant of
Pandoc.
* gnu/packages/bioinformatics.scm (r-bookdown)[propagated-inputs]: Remove
ghc-pandoc.
2018-03-22 17:07:15 +01:00
363ee7a3f4
gnu: pigx-chipseq: Update to 0.0.10.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.10.
[inputs]: Remove r-rcas and duplicate of snakemake; add r-biocparallel,
r-biostrings, r-dplyr, r-genomicalignments, rsamtools, r-s4vectors, r-tibble,
r-tidyr, r-htmlwidgets, and r-rmarkdown.
2018-03-21 11:52:56 +01:00
d7a11f1a8d
gnu: pigx-chipseq: Update to 0.0.9.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.9.
[inputs]: Add coreutils and grep.
2018-03-20 19:47:37 +01:00
4f1e4f33a0
gnu: pigx-bsseq: Update to 0.0.8.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
2018-03-20 14:56:44 +01:00
616446ffbf
gnu: pigx-rnaseq: Update to 0.0.3.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3.
[inputs]: Add gzip.
2018-03-20 12:20:51 +01:00
9dbdc830f6
gnu: pigx-bsseq: Update to 0.0.7.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7.
[inputs]: Add coreutils, sed, and grep.
2018-03-19 21:06:51 +01:00
096589035e
gnu: bismark: Fix references to gunzip.
...
* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to
gunzip executable.
[inputs]: Add gzip.
2018-03-19 21:06:51 +01:00
51237011bf
gnu: pigx-scrnaseq: Update to 0.0.3.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3.
[inputs]: Add coreutils and perl.
2018-03-19 21:06:50 +01:00
d8f08c85ad
gnu: pigx: Update to 0.0.2.
...
* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
2018-03-19 16:55:43 +01:00
d93a1c276b
gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1.
...
* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace
ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 16:55:43 +01:00
32b7ccf9b4
gnu: pigx-chipseq: Update to 0.0.8.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8.
[inputs]: Add python-magic, python-xlrd, and trim-galore.
[arguments]: Disable tests.
2018-03-19 11:07:55 +01:00
2915221bcb
gnu: pigx-scrnaseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:55 +01:00
9dcb4d22a4
gnu: pigx-bsseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:55 +01:00
fd757a8f21
gnu: pigx-chipseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:55 +01:00
1a29fc3ff9
gnu: pigx-rnaseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:54 +01:00
c1c9cc664b
gnu: Add pigx.
...
* gnu/packages/bioinformatics.scm (pigx): New variable.
2018-03-16 15:40:31 +01:00
fe52a215e5
gnu: pigx-rnaseq: Disable memory hungry test.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to
disable a memory hungry test.
2018-03-16 15:40:31 +01:00
46264c73a6
gnu: Add pigx-scrnaseq.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
2018-03-16 11:15:04 +01:00
b44437c549
gnu: kentutils: Build with mariadb.
...
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
2018-03-16 10:01:07 +01:00
32cbbac11a
gnu: Add Diversitree.
...
* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
2018-03-15 10:57:51 -04:00
fb94174fc3
gnu: Add pigx-bsseq.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
2018-03-11 20:01:53 +01:00
531afc8a89
gnu: Add pigx-chipseq.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
2018-03-11 20:01:53 +01:00
a539ad867d
gnu: r-rhdf5lib: Make build reproducible.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
2018-03-09 11:40:59 +01:00
22a0c65969
gnu: Add r-phangorn.
...
* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
2018-03-08 23:31:56 +01:00
53cc59a1d8
gnu: r-ape: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
2018-03-08 23:31:55 +01:00
84c195e505
gnu: r-dropbead: Update to 0-2.d746c6f.
...
* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
2018-03-08 18:53:49 +01:00
0bdd5b8ab7
gnu: Add pigx-rnaseq.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
2018-03-07 23:25:36 +01:00
c072cf57b9
gnu: samtools: Update to 1.7.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
2018-03-06 16:03:04 +01:00
727d847980
gnu: htslib: Update to 1.7.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
2018-03-06 16:03:04 +01:00
e325c89076
gnu: r-rhdf5: Make build reproducible.
...
* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
2018-03-06 16:03:04 +01:00
da49d13710
gnu: piranha: Declare a source file-name.
...
* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
2018-03-04 12:05:13 +02:00
d9a069c2d9
gnu: libdivsufsort: Declare a source file-name.
...
* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
2018-03-04 12:05:13 +02:00
Ricardo Wurmus