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2018-05-24gnu: Add fastp....* gnu/packages/bioinformatics.scm (fastp): New variable. Ricardo Wurmus
2018-05-23gnu: pigx-scrnaseq: Update to 0.0.4....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.4. Ricardo Wurmus
2018-05-22gnu: bismark: Patch bismark2report before installing....* gnu/packages/bioinformatics.scm (bismark)[arguments]: Patch file before installing it. Ricardo Wurmus
2018-05-19gnu: f-seq: Factorise ‘install’ phase....* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Let-bind more. Tobias Geerinckx-Rice
2018-05-17gnu: multiqc: Fix build....* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Add a ‘relax-requirements’ phase to fix building with python-matplotlib@2.2. Tobias Geerinckx-Rice
2018-05-12gnu: diamond: Update to 0.9.22....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.22. Ben Woodcroft
2018-05-09gnu: 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
2018-05-09gnu: 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
2018-05-01gnu: 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
2018-04-28gnu: roary: Update to 3.12.0....* gnu/packages/bioinformatics.scm (roary): Update to 3.12.0. Roel Janssen
2018-04-28gnu: star: Update to 2.6.0a....* gnu/packages/bioinformatics.scm (star): Update to 2.6.0a. Roel Janssen
2018-04-28gnu: multiqc: Update to 1.5....* gnu/packages/bioinformatics.scm (multiqc): Update to 1.5. Roel Janssen
2018-04-28gnu: express: Link with shared protobuf library....* gnu/packages/bioinformatics.scm (express): Link with shared protobuf library. Roel Janssen
2018-04-28gnu: bamtools: Update to 2.5.1....* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.1. Roel Janssen
2018-04-28gnu: taxtastic: Update to 0.8.5....* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.5. Roel Janssen
2018-04-27gnu: vsearch: Update to 2.8.0....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.8.0. Ben Woodcroft
2018-04-27gnu: diamond: Update to 0.9.21....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.21. Ben Woodcroft
2018-04-27gnu: bedops: Update to 2.4.33....* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.33. Roel Janssen
2018-04-27gnu: samtools: Update to 1.8....* gnu/packages/bioinformatics.scm (samtools): Update to 1.8. Roel Janssen
2018-04-27gnu: 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
2018-04-27gnu: htslib: Update to 1.8....* gnu/packages/bioinformatics.scm (htslib): Update to 1.8. Roel Janssen
2018-04-22gnu: pigx-chipseq: Update to 0.0.15....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.15. Ricardo Wurmus
2018-04-21gnu: 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
2018-04-21gnu: r-scran: Update to 1.6.9....* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.9. Ricardo Wurmus
2018-04-21gnu: r-hitc: Update to 1.22.1....* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.22.1. Ricardo Wurmus
2018-04-21gnu: r-ldblock: Update to 1.8.1....* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.8.1. Ricardo Wurmus
2018-04-21gnu: r-erma: Update to 0.10.1....* gnu/packages/bioinformatics.scm (r-erma): Update to 0.10.1. Ricardo Wurmus
2018-04-21gnu: r-gprofiler: Update to 0.6.6....* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.6. Ricardo Wurmus
2018-04-21gnu: r-ggbio: Update to 1.26.1....* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.26.1. Ricardo Wurmus
2018-04-21gnu: r-genomicalignments: Update to 1.14.2....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.2. Ricardo Wurmus
2018-04-21gnu: r-dexseq: Update to 1.24.4....* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.4. Ricardo Wurmus
2018-04-21gnu: 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
2018-04-06gnu: 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
2018-04-06gnu: htslib-for-sambamba: Fix build....* gnu/packages/bioinformatics.scm (htslib-for-sambamba)[arguments]: Do not inherit htslib arguments. Ricardo Wurmus
2018-03-30gnu: 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
2018-03-30gnu: mash: Update to 2.0....* gnu/packages/bioinformatics.scm (mash): Update to 2.0. Ben Woodcroft
2018-03-30gnu: mafft: Update to 7.394....* gnu/packages/bioinformatics.scm (mafft): Update to 7.394. Ben Woodcroft
2018-03-30gnu: diamond: Update to 0.9.19....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19. Ben Woodcroft
2018-03-29gnu: 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
2018-03-29gnu: kaiju: Update to 1.6.2....* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2; [inputs]: Add zlib. Roel Janssen
2018-03-25gnu: r-annotate: Update to 1.56.2....* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.2. Tobias Geerinckx-Rice
2018-03-22gnu: 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
2018-03-21gnu: 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
2018-03-20gnu: 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
2018-03-20gnu: pigx-bsseq: Update to 0.0.8....* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8. Ricardo Wurmus
2018-03-20gnu: pigx-rnaseq: Update to 0.0.3....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3. [inputs]: Add gzip. Ricardo Wurmus
2018-03-19gnu: 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
2018-03-19gnu: bismark: Fix references to gunzip....* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to gunzip executable. [inputs]: Add gzip. Ricardo Wurmus
2018-03-19gnu: 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
2018-03-19gnu: pigx: Update to 0.0.2....* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2. Ricardo Wurmus
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