| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2018-03-16 | gnu: Add pigx....* gnu/packages/bioinformatics.scm (pigx): New variable.
| Ricardo Wurmus |
| 2018-03-16 | gnu: pigx-rnaseq: Disable memory hungry test....* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to
disable a memory hungry test.
| Ricardo Wurmus |
| 2018-03-16 | gnu: Add pigx-scrnaseq....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
| Ricardo Wurmus |
| 2018-03-16 | gnu: kentutils: Build with mariadb....* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
| Ricardo Wurmus |
| 2018-03-15 | gnu: Add Diversitree....* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
| Leo Famulari |
| 2018-03-11 | gnu: Add pigx-bsseq....* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
| Ricardo Wurmus |
| 2018-03-11 | gnu: Add pigx-chipseq....* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
| Ricardo Wurmus |
| 2018-03-09 | gnu: r-rhdf5lib: Make build reproducible....* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
| Ricardo Wurmus |
| 2018-03-08 | gnu: Add r-phangorn....* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
| Ricardo Wurmus |
| 2018-03-08 | 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.
| Ricardo Wurmus |
| 2018-03-08 | gnu: r-dropbead: Update to 0-2.d746c6f....* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
| Ricardo Wurmus |
| 2018-03-07 | gnu: Add pigx-rnaseq....* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
| Ricardo Wurmus |
| 2018-03-06 | gnu: samtools: Update to 1.7....* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
| Ricardo Wurmus |
| 2018-03-06 | gnu: htslib: Update to 1.7....* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
| Ricardo Wurmus |
| 2018-03-06 | gnu: r-rhdf5: Make build reproducible....* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
| Ricardo Wurmus |
| 2018-03-04 | gnu: piranha: Declare a source file-name....* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
| Efraim Flashner |
| 2018-03-04 | gnu: libdivsufsort: Declare a source file-name....* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
| Efraim Flashner |
| 2018-03-04 | gnu: seek: Declare a source file-name....* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source
file-name.
| Efraim Flashner |
| 2018-03-04 | gnu: r-dropbead: Declare a source file-name....* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source
file-name.
| Efraim Flashner |
| 2018-03-03 | gnu: Add dropseq-tools....* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-picard-2.10.3....* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-htsjdk-2.10.1....* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-htsjdk-latest....* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-biojava-alignment-4.0....* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-biojava-phylo-4.0....* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
| Ricardo Wurmus |
| 2018-03-03 | gnu: Add java-biojava-core-4.0....* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
| Ricardo Wurmus |
