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* gnu: r-annotate: Update to 1.56.2.Tobias Geerinckx-Rice2018-03-25
| | | | * gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.2.
* gnu: r-bookdown: Do not propagate ghc-pandoc.Ricardo Wurmus2018-03-22
| | | | | | | | This package propagates r-rmarkdown, which propagates its own variant of Pandoc. * gnu/packages/bioinformatics.scm (r-bookdown)[propagated-inputs]: Remove ghc-pandoc.
* gnu: pigx-chipseq: Update to 0.0.10.Ricardo Wurmus2018-03-21
| | | | | | | * 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.
* gnu: pigx-chipseq: Update to 0.0.9.Ricardo Wurmus2018-03-20
| | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.9. [inputs]: Add coreutils and grep.
* gnu: pigx-bsseq: Update to 0.0.8.Ricardo Wurmus2018-03-20
| | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
* gnu: pigx-rnaseq: Update to 0.0.3.Ricardo Wurmus2018-03-20
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3. [inputs]: Add gzip.
* gnu: pigx-bsseq: Update to 0.0.7.Ricardo Wurmus2018-03-19
| | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7. [inputs]: Add coreutils, sed, and grep.
* gnu: bismark: Fix references to gunzip.Ricardo Wurmus2018-03-19
| | | | | | * gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to gunzip executable. [inputs]: Add gzip.
* gnu: pigx-scrnaseq: Update to 0.0.3.Ricardo Wurmus2018-03-19
| | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3. [inputs]: Add coreutils and perl.
* gnu: pigx: Update to 0.0.2.Ricardo Wurmus2018-03-19
| | | | * gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
* gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1.Ricardo Wurmus2018-03-19
| | | | | * gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
* gnu: pigx-chipseq: Update to 0.0.8.Ricardo Wurmus2018-03-19
| | | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8. [inputs]: Add python-magic, python-xlrd, and trim-galore. [arguments]: Disable tests.
* gnu: pigx-scrnaseq: Use pandoc-1.Ricardo Wurmus2018-03-19
| | | | | | * 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.
* gnu: pigx-bsseq: Use pandoc-1.Ricardo Wurmus2018-03-19
| | | | | | * 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.
* gnu: pigx-chipseq: Use pandoc-1.Ricardo Wurmus2018-03-19
| | | | | | * 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.
* gnu: pigx-rnaseq: Use pandoc-1.Ricardo Wurmus2018-03-19
| | | | | | * 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.
* gnu: Add pigx.Ricardo Wurmus2018-03-16
| | | | * gnu/packages/bioinformatics.scm (pigx): New variable.
* gnu: pigx-rnaseq: Disable memory hungry test.Ricardo Wurmus2018-03-16
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to disable a memory hungry test.
* gnu: Add pigx-scrnaseq.Ricardo Wurmus2018-03-16
| | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
* gnu: kentutils: Build with mariadb.Ricardo Wurmus2018-03-16
| | | | | * gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with mariadb.
* gnu: Add Diversitree.Leo Famulari2018-03-15
| | | | * gnu/packages/bioinformatics.scm (r-diversitree): New variable.
* gnu: Add pigx-bsseq.Ricardo Wurmus2018-03-11
| | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
* gnu: Add pigx-chipseq.Ricardo Wurmus2018-03-11
| | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
* gnu: r-rhdf5lib: Make build reproducible.Ricardo Wurmus2018-03-09
| | | | | * gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp and host system kernel version.
* gnu: Add r-phangorn.Ricardo Wurmus2018-03-08
| | | | * gnu/packages/bioinformatics.scm (r-phangorn): New variable.
* gnu: r-ape: Move to (gnu packages cran).Ricardo Wurmus2018-03-08
| | | | | * gnu/packages/bioinformatics.scm (r-ape): Move from here... * gnu/packages/cran.scm (r-ape): ...to here.
* gnu: r-dropbead: Update to 0-2.d746c6f.Ricardo Wurmus2018-03-08
| | | | * gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
* gnu: Add pigx-rnaseq.Ricardo Wurmus2018-03-07
| | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
* gnu: samtools: Update to 1.7.Ricardo Wurmus2018-03-06
| | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
* gnu: htslib: Update to 1.7.Ricardo Wurmus2018-03-06
| | | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.7. [arguments]: Remove field.
* gnu: r-rhdf5: Make build reproducible.Ricardo Wurmus2018-03-06
| | | | | * gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and host system information from settings file.
* gnu: piranha: Declare a source file-name.Efraim Flashner2018-03-04
| | | | | * gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source file-name.
* gnu: libdivsufsort: Declare a source file-name.Efraim Flashner2018-03-04
| | | | | * gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a source file-name.
* gnu: seek: Declare a source file-name.Efraim Flashner2018-03-04
| | | | | * gnu/packages/bioinformatics.scm (seek)[source]: Declare a source file-name.
* gnu: r-dropbead: Declare a source file-name.Efraim Flashner2018-03-04
| | | | | * gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source file-name.
* gnu: Add dropseq-tools.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
* gnu: Add java-picard-2.10.3.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
* gnu: Add java-htsjdk-2.10.1.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
* gnu: Add java-htsjdk-latest.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
* gnu: Add java-biojava-alignment-4.0.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
* gnu: Add java-biojava-phylo-4.0.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
* gnu: Add java-biojava-core-4.0.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
* gnu: Add java-biojava-alignment.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
* gnu: Add java-biojava-phylo.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
* gnu: Add java-forester-1.005.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
* gnu: Add java-forester.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (java-forester): New variable.
* gnu: Add java-biojava-core.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
* gnu: Add fastqc.Ricardo Wurmus2018-03-03
| | | | * gnu/packages/bioinformatics.scm (fastqc): New variable.
* gnu: cutadapt: Update to 1.16.Ricardo Wurmus2018-03-02
| | | | | | | * gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16. [source]: Fetch via git. [arguments]: Remove. [native-inputs]: Replace python-nose with python-pytest.
* gnu: r-scran: Update to 1.6.8.Ricardo Wurmus2018-03-01
| | | | * gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8.
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