| Age | Commit message (Expand) | Author |
|---|
| 2016-01-14 | 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 |
| 2016-01-13 | 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 |
| 2016-01-12 | gnu: Add fxtract....* gnu/packages/bioinformatics.scm (fxtract): New variable.
| Ben Woodcroft |
| 2016-01-11 | 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 |
| 2016-01-08 | 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 |
| 2016-01-07 | 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 |
| 2016-01-06 | 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 |
| 2015-12-29 | gnu: Add fraggenescan....* gnu/packages/bioinformatics.scm (fraggenescan): New variable.
| Ben Woodcroft |
| 2015-12-21 | 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 |
| 2015-12-11 | gnu: Add snap-aligner....* gnu/packages/bioinformatics.scm (snap-aligner): New variable.
| Ben Woodcroft |
| 2015-12-10 | gnu: python-biopython, python2-biopython: Update to 1.66....* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66.
[source]: Use PyPi instead of biopython.org.
| Ben Woodcroft |
| 2015-11-20 | gnu: preseq: Update to 2.0....* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
[source]: Add file-name field, remove patches.
[arguments]: Remove unused build phases, add make flags.
[inputs]: Add smithlab-cpp.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
file.
* gnu-system.am (dist_patch_DATA): Remove them.
| Ricardo Wurmus |
| 2015-11-20 | gnu: Add smithlab-cpp....* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
| Ricardo Wurmus |
| 2015-11-20 | gnu: edirect: Update home page....* gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing
slash to home page.
| Ricardo Wurmus |
| 2015-11-20 | gnu: sra-tools: Update to 2.5.4....* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.
| Ricardo Wurmus |
| 2015-11-20 | gnu: ncbi-vdb: Update to 2.5.4....* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4.
| Ricardo Wurmus |
| 2015-11-20 | gnu: ngs-java: Update to 1.2.2....* gnu/packages/bioinformatics.scm (ngs-java): Update to 1.2.2.
[arguments]: Remove build phase "fix-java-symlink-installation".
| Ricardo Wurmus |
| 2015-11-20 | gnu: ngs-sdk: Update to 1.2.2....* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2.
| Ricardo Wurmus |
| 2015-11-20 | gnu: bless: Build only for x86_64....* gnu/packages/bioinformatics.scm (bless): Add supported-systems field.
| Ricardo Wurmus |
| 2015-11-20 | gnu: htseq: Propagate numpy....* gnu/packages/bioinformatics.scm (htseq)[inputs]: Move python2-numpy
from here ...
[propagated-inputs]: ... to here.
| Ricardo Wurmus |
| 2015-11-12 | gnu: mosaik: Build only on x86_64....* gnu/packages/bioinformatics.scm (mosaik)[supported-systems]: Add
field.
| Ricardo Wurmus |
| 2015-11-06 | gnu: bless: Correct indentation and home-page....* gnu/packages/bioinformatics.scm (bless): Fix indentation.
[home-page]: Replace broken URL.
| Ricardo Wurmus |
| 2015-11-06 | gnu: Add BLESS....* gnu/packages/bioinformatics.scm (bless): New variable.
Co-authored-by: Diane Trout <diane@ghic.org>
| Ricardo Wurmus |
