| Commit message (Expand) | Author | Age | Files | Lines |
|---|
| * | 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 | 1 | -27/+12 |
| * | gnu: Add fxtract.•••* gnu/packages/bioinformatics.scm (fxtract): New variable.
| Ben Woodcroft | 2016-01-12 | 1 | -0/+66 |
| * | 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 | 1 | -14/+3 |
| * | gnu: bedtools: Use modify-phases.•••* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
| Ben Woodcroft | 2016-01-11 | 1 | -19/+19 |
| * | 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 | 1 | -0/+1 |
| * | gnu: Add genomation.•••* gnu/packages/bioinformatics.scm (r-genomation): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+43 |
| * | gnu: Add seqPattern.•••* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+26 |
| * | gnu: Add impute.•••* gnu/packages/bioinformatics.scm (r-impute): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+20 |
| * | gnu: Add BSgenome.•••* gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+30 |
| * | gnu: Add topGO.•••* gnu/packages/bioinformatics.scm (r-topgo): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+29 |
| * | gnu: Add GO.db.•••* gnu/packages/bioinformatics.scm (r-go-db): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+20 |
| * | gnu: Add GenomicFeatures.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+41 |
| * | gnu: Add rtracklayer.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+45 |
| * | gnu: Add GenomicAlignments.•••* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+33 |
| * | gnu: Add SummarizedExperiment.•••* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+29 |
| * | gnu: Add Rsamtools.•••* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+44 |
| * | gnu: Add Biostrings.•••* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+26 |
| * | gnu: Add BiocParallel.•••* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+24 |
| * | gnu: Add biomaRt.•••* gnu/packages/bioinformatics.scm (r-biomart): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+30 |
| * | gnu: Add AnnotationDbi.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+27 |
| * | gnu: Add Biobase.•••* gnu/packages/bioinformatics.scm (r-biobase): New variable.
| Ricardo Wurmus | 2016-01-07 | 1 | -0/+22 |
| * | gnu: edirect: Update to 3.50.•••* gnu/packages/bioinformatics.scm (edirect): Update to 3.50.
[native-inputs]: Remove "unzip".
| Ricardo Wurmus | 2016-01-07 | 1 | -5/+3 |
| * | 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 | 1 | -2/+2 |
| * | gnu: Add Jellyfish.•••* gnu/packages/bioinformatics.scm (jellyfish): New variable.
| Ricardo Wurmus | 2016-01-06 | 1 | -0/+50 |
| * | gnu: Add fraggenescan.•••* gnu/packages/bioinformatics.scm (fraggenescan): New variable.
| Ben Woodcroft | 2015-12-29 | 1 | -0/+81 |
| * | gnu: Add GenomicRanges.•••* gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
| Ricardo Wurmus | 2015-12-21 | 1 | -0/+28 |
| * | gnu: Add XVector.•••* gnu/packages/bioinformatics.scm (r-xvector): New variable.
| Ricardo Wurmus | 2015-12-21 | 1 | -0/+37 |
| * | gnu: Add GenomeInfoDb.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
| Ricardo Wurmus | 2015-12-21 | 1 | -0/+27 |
| * | gnu: Add IRanges.•••* gnu/packages/bioinformatics.scm (r-iranges): New variable.
| Ricardo Wurmus | 2015-12-21 | 1 | -0/+30 |
| * | gnu: Add S4Vectors.•••* gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
| Ricardo Wurmus | 2015-12-21 | 1 | -0/+28 |
| * | gnu: Add BiocGenerics.•••* gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
| Ricardo Wurmus | 2015-12-21 | 1 | -0/+21 |
| * | gnu: Add r-acsnminer.•••* gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
| Ricardo Wurmus | 2015-12-21 | 1 | -0/+26 |
| * | 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 | 1 | -3/+20 |
| * | gnu: Add snap-aligner.•••* gnu/packages/bioinformatics.scm (snap-aligner): New variable.
| Ben Woodcroft | 2015-12-11 | 1 | -0/+37 |
| * | 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 | 2015-12-10 | 1 | -5/+4 |
| * | 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 | 1 | -25/+18 |
| * | gnu: Add smithlab-cpp.•••* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
| Ricardo Wurmus | 2015-11-20 | 1 | -0/+53 |
| * | gnu: edirect: Update home page.•••* gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing
slash to home page.
| Ricardo Wurmus | 2015-11-20 | 1 | -1/+1 |
| * | gnu: sra-tools: Update to 2.5.4.•••* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.
| Ricardo Wurmus | 2015-11-20 | 1 | -2/+2 |
| * | gnu: ncbi-vdb: Update to 2.5.4.•••* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4.
| Ricardo Wurmus | 2015-11-20 | 1 | -16/+2 |
| * | 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 | 1 | -20/+2 |
| * | gnu: ngs-sdk: Update to 1.2.2.•••* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2.
| Ricardo Wurmus | 2015-11-20 | 1 | -2/+2 |
| * | gnu: bless: Build only for x86_64.•••* gnu/packages/bioinformatics.scm (bless): Add supported-systems field.
| Ricardo Wurmus | 2015-11-20 | 1 | -0/+1 |
| * | gnu: htseq: Propagate numpy.•••* gnu/packages/bioinformatics.scm (htseq)[inputs]: Move python2-numpy
from here ...
[propagated-inputs]: ... to here.
| Ricardo Wurmus | 2015-11-20 | 1 | -3/+5 |
| * | gnu: mosaik: Build only on x86_64.•••* gnu/packages/bioinformatics.scm (mosaik)[supported-systems]: Add
field.
| Ricardo Wurmus | 2015-11-12 | 1 | -0/+1 |
| * | gnu: bless: Correct indentation and home-page.•••* gnu/packages/bioinformatics.scm (bless): Fix indentation.
[home-page]: Replace broken URL.
| Ricardo Wurmus | 2015-11-06 | 1 | -3/+3 |
| * | gnu: Add BLESS.•••* gnu/packages/bioinformatics.scm (bless): New variable.
Co-authored-by: Diane Trout <diane@ghic.org>
| Ricardo Wurmus | 2015-11-06 | 1 | -0/+83 |
| * | gnu: hisat: Disable build on non-x86_64.•••* gnu/packages/bioinformatics.scm (hisat)[supported-systems]: Add field.
| Ricardo Wurmus | 2015-11-02 | 1 | -0/+3 |
| * | gnu: Add express-beta-diversity.•••* gnu/packages/bioinformatics.scm (express-beta-diversity): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Ben Woodcroft | 2015-11-02 | 1 | -0/+45 |
| * | gnu: pbtranscript-tofu: Update to 2.2.3.•••* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Update to 2.2.3.
[source]: Remove bundled Cython sources in a snippet. Replace
".tar.gz" extension in file-name field with "-checkout".
[arguments]: Replace "enter-directory-and-clean-up" phase with
"enter-directory" phase, and add "patch-setuppy" phase.
[inputs]: Add python2-h5py. Move python2-cython ...
[native-inputs]: ... to this field.
| Ricardo Wurmus | 2015-10-28 | 1 | -27/+28 |
