| Age | Commit message (Expand) | Author |
|---|
| 2018-05-09 | gnu: bismark: Update to 0.19.1....* gnu/packages/bioinformatics.scm (bismark): Update to 0.19.1.
[source]: Fetch from git; remove non-free software in snippet.
[arguments]: Update install phase.
| Ricardo Wurmus |
| 2018-05-09 | gnu: trim-galore: Update to 0.4.5....* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.4.5.
[source]: Fetch from git.
[arguments]: Remove custom unpack phase.
| Ricardo Wurmus |
| 2018-05-01 | gnu: Use HTTPS for www.boost.org....* gnu/packages/bioinformatics.scm (libgff)[license]: Use HTTPS.
* gnu/packages/boost.scm (boost-sync)[license]: Likewise.
(boost)[license]: Likewise.
[home-page]: Likewise, and use canonical ‘www’ subdomain.
| Tobias Geerinckx-Rice |
| 2018-04-28 | gnu: roary: Update to 3.12.0....* gnu/packages/bioinformatics.scm (roary): Update to 3.12.0.
| Roel Janssen |
| 2018-04-28 | gnu: star: Update to 2.6.0a....* gnu/packages/bioinformatics.scm (star): Update to 2.6.0a.
| Roel Janssen |
| 2018-04-28 | gnu: multiqc: Update to 1.5....* gnu/packages/bioinformatics.scm (multiqc): Update to 1.5.
| Roel Janssen |
| 2018-04-28 | gnu: express: Link with shared protobuf library....* gnu/packages/bioinformatics.scm (express): Link with shared protobuf
library.
| Roel Janssen |
| 2018-04-28 | gnu: bamtools: Update to 2.5.1....* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.1.
| Roel Janssen |
| 2018-04-28 | gnu: taxtastic: Update to 0.8.5....* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.5.
| Roel Janssen |
| 2018-04-27 | gnu: vsearch: Update to 2.8.0....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.8.0.
| Ben Woodcroft |
| 2018-04-27 | gnu: diamond: Update to 0.9.21....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.21.
| Ben Woodcroft |
| 2018-04-27 | gnu: bedops: Update to 2.4.33....* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.33.
| Roel Janssen |
| 2018-04-27 | gnu: samtools: Update to 1.8....* gnu/packages/bioinformatics.scm (samtools): Update to 1.8.
| Roel Janssen |
| 2018-04-27 | gnu: bcftools: Update to 1.8....* gnu/packages/bioinformatics.scm (bcftools): Update to 1.8.
* gnu/local.mk: Remove patch.
* gnu/packages/patches/bcftools-regidx-unsigned-char.patch: Remove file.
| Roel Janssen |
| 2018-04-27 | gnu: htslib: Update to 1.8....* gnu/packages/bioinformatics.scm (htslib): Update to 1.8.
| Roel Janssen |
| 2018-04-22 | gnu: pigx-chipseq: Update to 0.0.15....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.15.
| Ricardo Wurmus |
| 2018-04-21 | gnu: r-seurat: Update to 2.3.0....* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.0.
[propagated-inputs]: Add r-cluster, r-dosnow, r-fitdistrplus, r-foreach,
r-lmtest, r-png, and r-rann.
| Ricardo Wurmus |
| 2018-04-21 | gnu: r-scran: Update to 1.6.9....* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.9.
| Ricardo Wurmus |
| 2018-04-21 | gnu: r-hitc: Update to 1.22.1....* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.22.1.
| Ricardo Wurmus |
| 2018-04-21 | gnu: r-ldblock: Update to 1.8.1....* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.8.1.
| Ricardo Wurmus |
| 2018-04-21 | gnu: r-erma: Update to 0.10.1....* gnu/packages/bioinformatics.scm (r-erma): Update to 0.10.1.
| Ricardo Wurmus |
| 2018-04-21 | gnu: r-gprofiler: Update to 0.6.6....* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.6.
| Ricardo Wurmus |
| 2018-04-21 | gnu: r-ggbio: Update to 1.26.1....* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.26.1.
| Ricardo Wurmus |
| 2018-04-21 | gnu: r-genomicalignments: Update to 1.14.2....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.2.
| Ricardo Wurmus |
| 2018-04-21 | gnu: r-dexseq: Update to 1.24.4....* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.4.
| Ricardo Wurmus |
| 2018-04-21 | gnu: r-vegan: Update to 2.5-1....* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-1.
[propagated-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2018-04-06 | 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.
| Ricardo Wurmus |
| 2018-04-06 | gnu: htslib-for-sambamba: Fix build....* gnu/packages/bioinformatics.scm (htslib-for-sambamba)[arguments]: Do not
inherit htslib arguments.
| Ricardo Wurmus |
| 2018-03-30 | 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>
| Roel Janssen |
| 2018-03-30 | gnu: mash: Update to 2.0....* gnu/packages/bioinformatics.scm (mash): Update to 2.0.
| Ben Woodcroft |
| 2018-03-30 | gnu: mafft: Update to 7.394....* gnu/packages/bioinformatics.scm (mafft): Update to 7.394.
| Ben Woodcroft |
| 2018-03-30 | gnu: diamond: Update to 0.9.19....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19.
| Ben Woodcroft |
| 2018-03-29 | gnu: r-mutationalpatterns: Update to 1.4.3....* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3;
[propagated-inputs]: Remove r-gridextra.
| Roel Janssen |
| 2018-03-29 | gnu: kaiju: Update to 1.6.2....* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2;
[inputs]: Add zlib.
| Roel Janssen |
| 2018-03-25 | gnu: r-annotate: Update to 1.56.2....* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.2.
| Tobias Geerinckx-Rice |
| 2018-03-22 | 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.
| Ricardo Wurmus |
| 2018-03-21 | 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.
| Ricardo Wurmus |
| 2018-03-20 | gnu: pigx-chipseq: Update to 0.0.9....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.9.
[inputs]: Add coreutils and grep.
| Ricardo Wurmus |
| 2018-03-20 | gnu: pigx-bsseq: Update to 0.0.8....* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
| Ricardo Wurmus |
| 2018-03-20 | gnu: pigx-rnaseq: Update to 0.0.3....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3.
[inputs]: Add gzip.
| Ricardo Wurmus |
| 2018-03-19 | 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.
| Ricardo Wurmus |
| 2018-03-19 | gnu: bismark: Fix references to gunzip....* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to
gunzip executable.
[inputs]: Add gzip.
| Ricardo Wurmus |
| 2018-03-19 | gnu: pigx-scrnaseq: Update to 0.0.3....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3.
[inputs]: Add coreutils and perl.
| Ricardo Wurmus |
| 2018-03-19 | gnu: pigx: Update to 0.0.2....* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
| Ricardo Wurmus |
| 2018-03-19 | 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.
| Ricardo Wurmus |
| 2018-03-19 | 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.
| Ricardo Wurmus |
| 2018-03-19 | 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.
| Ricardo Wurmus |
| 2018-03-19 | 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.
| Ricardo Wurmus |
| 2018-03-19 | 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.
| Ricardo Wurmus |
| 2018-03-19 | 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.
| Ricardo Wurmus |
