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2018-04-30Merge branch 'master' into core-updatesMark H Weaver
2018-04-28gnu: roary: Update to 3.12.0.Roel Janssen
* gnu/packages/bioinformatics.scm (roary): Update to 3.12.0.
2018-04-28gnu: star: Update to 2.6.0a.Roel Janssen
* gnu/packages/bioinformatics.scm (star): Update to 2.6.0a.
2018-04-28gnu: multiqc: Update to 1.5.Roel Janssen
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.5.
2018-04-28gnu: express: Link with shared protobuf library.Roel Janssen
* gnu/packages/bioinformatics.scm (express): Link with shared protobuf library.
2018-04-28gnu: bamtools: Update to 2.5.1.Roel Janssen
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.1.
2018-04-28gnu: taxtastic: Update to 0.8.5.Roel Janssen
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.5.
2018-04-27gnu: vsearch: Update to 2.8.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.8.0.
2018-04-27gnu: diamond: Update to 0.9.21.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.21.
2018-04-27gnu: bedops: Update to 2.4.33.Roel Janssen
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.33.
2018-04-27gnu: samtools: Update to 1.8.Roel Janssen
* gnu/packages/bioinformatics.scm (samtools): Update to 1.8.
2018-04-27gnu: bcftools: Update to 1.8.Roel Janssen
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.8. * gnu/local.mk: Remove patch. * gnu/packages/patches/bcftools-regidx-unsigned-char.patch: Remove file.
2018-04-27gnu: htslib: Update to 1.8.Roel Janssen
* gnu/packages/bioinformatics.scm (htslib): Update to 1.8.
2018-04-22gnu: pigx-chipseq: Update to 0.0.15.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.15.
2018-04-21gnu: r-seurat: Update to 2.3.0.Ricardo Wurmus
* 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.
2018-04-21gnu: r-scran: Update to 1.6.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.9.
2018-04-21gnu: r-hitc: Update to 1.22.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.22.1.
2018-04-21gnu: r-ldblock: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.8.1.
2018-04-21gnu: r-erma: Update to 0.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.10.1.
2018-04-21gnu: r-gprofiler: Update to 0.6.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.6.
2018-04-21gnu: r-ggbio: Update to 1.26.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.26.1.
2018-04-21gnu: r-genomicalignments: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.2.
2018-04-21gnu: r-dexseq: Update to 1.24.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.4.
2018-04-21gnu: r-vegan: Update to 2.5-1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-1. [propagated-inputs]: Add r-knitr.
2018-04-10Merge branch 'master' into core-updatesMark H Weaver
2018-04-06gnu: sambamba: Update to 0.6.7-10-g223fa20.Ricardo Wurmus
* 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.
2018-04-06gnu: htslib-for-sambamba: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib-for-sambamba)[arguments]: Do not inherit htslib arguments.
2018-03-30gnu: Add delly.Roel Janssen
* 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>
2018-03-30gnu: mash: Update to 2.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (mash): Update to 2.0.
2018-03-30gnu: mafft: Update to 7.394.Ben Woodcroft
* gnu/packages/bioinformatics.scm (mafft): Update to 7.394.
2018-03-30gnu: diamond: Update to 0.9.19.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19.
2018-03-29Merge branch 'master' into core-updatesMarius Bakke
2018-03-29gnu: r-mutationalpatterns: Update to 1.4.3.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3; [propagated-inputs]: Remove r-gridextra.
2018-03-29gnu: kaiju: Update to 1.6.2.Roel Janssen
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2; [inputs]: Add zlib.
2018-03-27gnu: Use invoke and return #t from all builders.Mark H Weaver
* gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/audio.scm, gnu/packages/avr.scm, gnu/packages/base.scm, gnu/packages/bioinformatics.scm, gnu/packages/certs.scm, gnu/packages/check.scm, gnu/packages/code.scm, gnu/packages/commencement.scm, gnu/packages/dictionaries.scm, gnu/packages/docbook.scm, gnu/packages/emacs.scm, gnu/packages/embedded.scm, gnu/packages/fonts.scm, gnu/packages/games.scm, gnu/packages/gnome.scm, gnu/packages/gnu-doc.scm, gnu/packages/guile.scm, gnu/packages/hurd.scm, gnu/packages/javascript.scm, gnu/packages/libreoffice.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm, gnu/packages/lxde.scm, gnu/packages/mail.scm, gnu/packages/markup.scm, gnu/packages/mate.scm, gnu/packages/pkg-config.scm, gnu/packages/qt.scm, gnu/packages/rust.scm, gnu/packages/scheme.scm, gnu/packages/sdl.scm, gnu/packages/statistics.scm, gnu/packages/syncthing.scm, gnu/packages/tex.scm, gnu/packages/web.scm, gnu/packages/wine.scm, gnu/packages/xfce.scm: In the builders of packages using 'trivial-build-system', use invoke where appropriate, raise exceptions on errors, and otherwise return #t.
2018-03-25gnu: r-annotate: Update to 1.56.2.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.2.
2018-03-22gnu: r-bookdown: Do not propagate ghc-pandoc.Ricardo Wurmus
This package propagates r-rmarkdown, which propagates its own variant of Pandoc. * gnu/packages/bioinformatics.scm (r-bookdown)[propagated-inputs]: Remove ghc-pandoc.
2018-03-21gnu: pigx-chipseq: Update to 0.0.10.Ricardo Wurmus
* 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.
2018-03-20gnu: pigx-chipseq: Update to 0.0.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.9. [inputs]: Add coreutils and grep.
2018-03-20Merge branch 'master' into core-updatesMark H Weaver
2018-03-20gnu: pigx-bsseq: Update to 0.0.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
2018-03-20gnu: pigx-rnaseq: Update to 0.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3. [inputs]: Add gzip.
2018-03-20Merge branch 'master' into core-updatesMark H Weaver
2018-03-19gnu: pigx-bsseq: Update to 0.0.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7. [inputs]: Add coreutils, sed, and grep.
2018-03-19gnu: bismark: Fix references to gunzip.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to gunzip executable. [inputs]: Add gzip.
2018-03-19gnu: pigx-scrnaseq: Update to 0.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3. [inputs]: Add coreutils and perl.
2018-03-19gnu: pigx: Update to 0.0.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
2018-03-19gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19gnu: pigx-chipseq: Update to 0.0.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8. [inputs]: Add python-magic, python-xlrd, and trim-galore. [arguments]: Disable tests.
2018-03-19gnu: pigx-scrnaseq: Use pandoc-1.Ricardo Wurmus
* 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.
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