| Commit message (Expand) | Author | Age |
|---|
| * | gnu: macs: Update to 2.1.0.20151222.•••* gnu/packages/bioinformatics.scm (macs): Update to 2.1.0.20151222.
| Ricardo Wurmus | 2016-02-12 |
| * | gnu: macs: Use "pypi-uri".•••* gnu/packages/bioinformatics.scm (macs)[source]: Use "pypi-uri" to
build source URI.
| Ricardo Wurmus | 2016-02-12 |
| * | gnu: Update sortmerna to 2.1.•••* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.
| Ben J. Woodcroft | 2016-02-02 |
| * | gnu: sra-tools: Update to 2.5.7.•••* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.
| Ben Woodcroft | 2016-01-26 |
| * | gnu: ncbi-vdb: Update to 2.5.7.•••gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.
| Ben Woodcroft | 2016-01-26 |
| * | gnu: ngs-sdk: Update to 1.2.3.•••gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.
| Ben Woodcroft | 2016-01-26 |
| * | gnu: Add sortmerna.•••* gnu/packages/bioinformatics.scm (sortmerna): New variable.
| Ben Woodcroft | 2016-01-25 |
| * | gnu: Add cufflinks.•••* gnu/packages/bioinformatics.scm (cufflinks): New variable.
| Ricardo Wurmus | 2016-01-23 |
| * | gnu: Add TopHat.•••* gnu/packages/bioinformatics.scm (tophat): New variable.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
| Ricardo Wurmus | 2016-01-23 |
| * | gnu: star: Update to 2.5.1b.•••* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b.
[source]: Remove bundled htslib sources and pre-built binaries.
[arguments]: Add phase "do-not-use-bundled-htslib".
[inputs]: Add "htslib".
| Ricardo Wurmus | 2016-01-23 |
| * | gnu: star: Use "modify-phases" syntax.•••* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
syntax.
| Ricardo Wurmus | 2016-01-23 |
| * | gnu: r-qtl: Update to 1.38-4.•••* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.
| Pjotr Prins | 2016-01-21 |
| * | gnu: samtools-0.1: Adapt to changes in "samtools" variable.•••* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add
"LIBCURSES" make flag; delete "configure" phase; disable tests outside
of "substitute-keyword-arguments".
| Ricardo Wurmus | 2016-01-16 |
| * | gnu: r-go-db: Add missing input.•••* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add
"r-annotationdbi".
| Ricardo Wurmus | 2016-01-14 |
| * | gnu: bowtie: Update to 2.2.6.•••* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6.
[source]: Remove patch; do not set CC and CPP variables.
[inputs]: Add "tbb".
[arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom
"install" phase.
* gnu/packages/patches/bowtie-fix-makefile.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove patch file.
| Ricardo Wurmus | 2016-01-14 |
| * | gnu: orfm: Update to 0.5.3.•••* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.
| Ben Woodcroft | 2016-01-14 |
| * | gnu: samtools: Update to 1.3.•••* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.
[arguments]: Enable tests for all architectures; set ncurses in
configure-flags instead of make-flags; simplify "patch-tests" phase;
restore "configure" phase.
| Ricardo Wurmus | 2016-01-13 |
| * | gnu: Add fxtract.•••* gnu/packages/bioinformatics.scm (fxtract): New variable.
| Ben Woodcroft | 2016-01-12 |
| * | gnu: bedtools: Update to 2.25.0.•••* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0.
[source]: Remove patch merged upstream.
[arguments]: Use 'modify-phases'. Remove
'patch-makefile-SHELL-definition' phase.
* gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
| Ben Woodcroft | 2016-01-11 |
| * | gnu: bedtools: Use modify-phases.•••* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
| Ben Woodcroft | 2016-01-11 |
| * | gnu: Add missing (gnu packages gcc) import.•••* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is
required by 'r-impute' for 'gfortran'.
| Mathieu Lirzin | 2016-01-08 |
| * | gnu: Add genomation.•••* gnu/packages/bioinformatics.scm (r-genomation): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add seqPattern.•••* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add impute.•••* gnu/packages/bioinformatics.scm (r-impute): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add BSgenome.•••* gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add topGO.•••* gnu/packages/bioinformatics.scm (r-topgo): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add GO.db.•••* gnu/packages/bioinformatics.scm (r-go-db): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add GenomicFeatures.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add rtracklayer.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add GenomicAlignments.•••* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add SummarizedExperiment.•••* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add Rsamtools.•••* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add Biostrings.•••* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add BiocParallel.•••* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add biomaRt.•••* gnu/packages/bioinformatics.scm (r-biomart): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add AnnotationDbi.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add Biobase.•••* gnu/packages/bioinformatics.scm (r-biobase): New variable.
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: edirect: Update to 3.50.•••* gnu/packages/bioinformatics.scm (edirect): Update to 3.50.
[native-inputs]: Remove "unzip".
| Ricardo Wurmus | 2016-01-07 |
| * | gnu: Add and use default IcedTea.•••* gnu/packages/java.scm (icedtea): New variable.
(swt)[native-inputs]: Replace "icedtea6" with "icedtea".
* gnu/packages/bioinformatics.scm (htsjdk)[native-inputs]: Likewise.
(ngs-java)[inputs]: Likewise.
* gnu/packages/kodi.scm (kodi)[native-inputs]: Replace "icedtea7" with
"icedtea".
* gnu/packages/ruby.scm (ruby-rjb)[native-inputs]: Replace "icedtea7"
with "icedtea".
| Ricardo Wurmus | 2016-01-06 |
| * | gnu: Add Jellyfish.•••* gnu/packages/bioinformatics.scm (jellyfish): New variable.
| Ricardo Wurmus | 2016-01-06 |
| * | gnu: Add fraggenescan.•••* gnu/packages/bioinformatics.scm (fraggenescan): New variable.
| Ben Woodcroft | 2015-12-29 |
| * | gnu: Add GenomicRanges.•••* gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
| Ricardo Wurmus | 2015-12-21 |
| * | gnu: Add XVector.•••* gnu/packages/bioinformatics.scm (r-xvector): New variable.
| Ricardo Wurmus | 2015-12-21 |
| * | gnu: Add GenomeInfoDb.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
| Ricardo Wurmus | 2015-12-21 |
| * | gnu: Add IRanges.•••* gnu/packages/bioinformatics.scm (r-iranges): New variable.
| Ricardo Wurmus | 2015-12-21 |
| * | gnu: Add S4Vectors.•••* gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
| Ricardo Wurmus | 2015-12-21 |
| * | gnu: Add BiocGenerics.•••* gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
| Ricardo Wurmus | 2015-12-21 |
| * | gnu: Add r-acsnminer.•••* gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
| Ricardo Wurmus | 2015-12-21 |
| * | gnu: mafft: Update to 7.267.•••* gnu/packages/bioinformatics.scm (mafft): Update to 7.267.
[arguments]: Don't include mafft-homologs manpage.
[inputs]: Add gawk and grep.
[propagated-inputs]: Add coreutils.
| Ben Woodcroft | 2015-12-21 |
| * | gnu: Add snap-aligner.•••* gnu/packages/bioinformatics.scm (snap-aligner): New variable.
| Ben Woodcroft | 2015-12-11 |