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path: root/gnu/packages/bioinformatics.scm
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2016-10-02gnu: vsearch: Update to 2.1.2....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.2. Ben Woodcroft
2016-09-28gnu: sra-tools: Fix build on i686....* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Pass "VDB_LIBDIR" in make-flags; dynamically link libmagic. Ricardo Wurmus
2016-09-27gnu: python-plastid: Update to 1.4.6....* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): Update to 1.4.6. [propagated-inputs]: Add python-termcolor. Ben J Woodcroft
2016-09-27gnu: python-pysam: Enable tests....* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from PyPi to source archive due to missing test data. [arguments]: Add check phase after install. [native-inputs]: Add python-nose, samtools and bcftools. Marius Bakke
2016-09-27gnu: python-pysam: Delete bundled htslib....* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet to delete htslib. [arguments]: Add htslib flags in 'set-flags phase. [propagated-inputs]: New field. Add htslib. Marius Bakke
2016-09-27gnu: python-pysam: Use 'modify-phases'....* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Use 'modify-phases'. Marius Bakke
2016-09-27gnu: Add bcftools....* gnu/packages/bioinformatics.scm (bcftools): New variable. Marius Bakke
2016-09-27gnu: python2-pbcore: Update to 1.2.10....* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.10. [propagated-inputs]: New field. Add python2-pyxb. Marius Bakke
2016-09-27gnu: python-pysam: Update to 0.9.1.4....* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): Update to 0.9.1.4. Marius Bakke
2016-09-26gnu: ncbi-vdb: Only build on i686 and x86_64....* gnu/packages/bioinformatics.scm (ncbi-vdb)[supported-systems]: Only build on i686 and x86_64. [arguments]: Add mandatory "-msse2" flag to CFLAGS. Ricardo Wurmus
2016-09-26gnu: vsearch: Update to 2.1.1....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.1. Ben Woodcroft
2016-09-26gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene....* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): New variable. Ricardo Wurmus
2016-09-26gnu: Add r-grohmm....* gnu/packages/bioinformatics.scm (r-grohmm): New variable. Ricardo Wurmus
2016-09-26gnu: Add r-systempiper....* gnu/packages/bioinformatics.scm (r-systempiper): New variable. Ricardo Wurmus
2016-09-26gnu: Add r-shortread....* gnu/packages/bioinformatics.scm (r-shortread): New variable. Ricardo Wurmus
2016-09-26gnu: Add r-gostats....* gnu/packages/bioinformatics.scm (r-gostats): New variable. Ricardo Wurmus
2016-09-26gnu: Add r-category....* gnu/packages/bioinformatics.scm (r-category): New variable. Ricardo Wurmus
2016-09-26gnu: Add r-gseabase....* gnu/packages/bioinformatics.scm (r-gseabase): New variable. Ricardo Wurmus
2016-09-26gnu: Add r-rbgl....* gnu/packages/bioinformatics.scm (r-rbgl): New variable. Ricardo Wurmus
2016-09-26gnu: Add r-annotationforge....* gnu/packages/bioinformatics.scm (r-annotationforge): New variable. Ricardo Wurmus
2016-09-26gnu: Add r-deseq2....* gnu/packages/bioinformatics.scm (r-deseq2): New variable. Ricardo Wurmus
2016-09-26gnu: Add r-genefilter....* gnu/packages/bioinformatics.scm (r-genefilter): New variable. Ricardo Wurmus
2016-09-26gnu: Add r-geneplotter....* gnu/packages/bioinformatics.scm (r-geneplotter): New variable. Ricardo Wurmus
2016-09-26gnu: Add r-annotate....* gnu/packages/bioinformatics.scm (r-annotate): New variable. Ricardo Wurmus
2016-09-23gnu: sra-tools: Update to 2.7.0....* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.7.0. Ricardo Wurmus
2016-09-23gnu: ncbi-vdb: Update to 2.7.0....* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.7.0. Ricardo Wurmus
2016-09-23gnu: ngs-sdk: Update to 1.2.5....* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.5. Ricardo Wurmus
2016-09-22gnu: plink: Set endian-ness on more architectures....* gnu/packages/patches/plink-endian-detection.patch: New file. * gnu/packages/bioinformatics.scm (plink)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Register it. Efraim Flashner
2016-09-22gnu: prank: Allow building on 32-bit machines....* gnu/packages/bioinformatics.scm (prank)[arguments]: Add a phase removing the '-m64' compiler flag. Efraim Flashner
2016-09-22gnu: diamond: Update to 0.8.22....* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.22. Ben Woodcroft
2016-09-21gnu: jellyfish: Limit to x86_64....* gnu/packages/bioinformatics.scm (jellyfish)[supported-systems}: New field, limit support to x86_64. Efraim Flashner
2016-09-21gnu: vsearch: Update to 2.1.0....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.0. Ben Woodcroft
2016-09-19gnu: Add r-biocinstaller....* gnu/packages/bioinformatics.scm (r-biocinstaller): New variable. Roel Janssen
2016-09-19gnu: python-biom-format: Move inputs to propagated-inputs....* gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format) [inputs]: Move all from here ... [propagated-inputs]: ... to here. Ben Woodcroft
2016-09-19gnu: seqmagick: Use BioPython 1.66....* gnu/packages/bioinformatics.scm (seqmagick)[inputs]: Use python2-biopython-1.66 instead of python2-biopython. Ben Woodcroft
2016-09-19gnu: Add python2-biopython-1.66....* gnu/packages/bioinformatics.scm (python2-biopython-1.66): New variable. Ben Woodcroft
2016-09-19gnu: python-biopython: Use 'python2-variant'....* gnu/packages/bioinformatics.scm (python-biopython)[properties]: New field. [native-inputs]: Remove field. (python-biopython): Use 'strip-python-variant'. Ben Woodcroft
2016-09-19gnu: python-biopython: Update to 1.68....* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.68. [arguments]: New field. Ben Woodcroft
2016-09-13gnu: Add seqtk....* gnu/packages/bioinformatics.scm (seqtk): New variable. Ben J Woodcroft
2016-09-12gnu: bowtie: Update to 2.2.9....* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.9. Leo Famulari
2016-09-12gnu: r-org-mm-eg-db: Update to 3.3.0....* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.3.0. Ricardo Wurmus
2016-09-12gnu: r-org-dm-eg-db: Update to 3.3.0....* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.3.0. Ricardo Wurmus
2016-09-12gnu: r-org-ce-eg-db: Update to 3.3.0....* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.3.0. Ricardo Wurmus
2016-09-12gnu: r-org-hs-eg-db: Update to 3.3.0....* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.3.0. Ricardo Wurmus
2016-09-12gnu: r-go-db: Update to 3.3.0....* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.3.0. Ricardo Wurmus
2016-09-12gnu: r-biocparallel: Update to 1.6.6....* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.6. Ricardo Wurmus
2016-09-12gnu: r-genomicranges: Update to 1.24.3....* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.3. Ricardo Wurmus
2016-09-12gnu: r-limma: Update to 3.28.21....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.21. Ricardo Wurmus
2016-09-12gnu: r-variantannotation: Update to 1.18.7....* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.7. Ricardo Wurmus
2016-09-12gnu: r-genomeinfodb: Update to 1.8.7....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.7. Ricardo Wurmus
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