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path: root/gnu/packages/bioinformatics.scm
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2017-08-31gnu: bioinformatics: Work around more "dotless @INC" build failures....* gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add 'set-perl-search-path' phase. Ben Woodcroft
2017-08-31gnu: metabat: Update to 2.11.3....* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.3. [source]: Use git-fetch. Remove boost-related patch. * gnu/packages/patches/metabat-fix-boost-issue.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Ben Woodcroft
2017-08-30gnu: multiqc: Update to 1.2....* gnu/packages/bioinformatics.scm (multiqc): Update to 1.2. [source]: Remove patches. [arguments]: Remove to enable tests. [propagated-inputs]: Add python-spectra, python-requests, python-markdown, python-lzstring. * gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. Ricardo Wurmus
2017-08-21Merge branch 'master' into core-updatesMarius Bakke
2017-08-20gnu: Add r-annotationfilter....* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable. Ricardo Wurmus
2017-08-17gnu: Add r-methylkit....* gnu/packages/bioinformatics.scm (r-methylkit): New variable. Ricardo Wurmus
2017-08-17gnu: Add r-qvalue....* gnu/packages/bioinformatics.scm (r-qvalue): New variable. Ricardo Wurmus
2017-08-17gnu: Add r-fastseg....* gnu/packages/bioinformatics.scm (r-fastseg): New variable. Ricardo Wurmus
2017-08-17gnu: Add r-annotationhub....* gnu/packages/bioinformatics.scm (r-annotationhub): New variable. Ricardo Wurmus
2017-08-17gnu: Add r-interactivedisplaybase....* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): New variable. Ricardo Wurmus
2017-08-16gnu: r-mzr: Fix building on aarch64 and armhf....* gnu/packages/bioinformatics.scm (r-mzr)[inputs]: Add boost. Efraim Flashner
2017-08-15gnu: diamond: Update to 0.9.10....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.10. Ben Woodcroft
2017-08-15gnu: bcftools: Fix building on aarch64....* gnu/packages/patches/bcftools-regidx-unsigned-char.patch: New file. * gnu/packages/bioinformatics.scm (bcftools)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Register it. Efraim Flashner
2017-08-15Merge branch 'master' into core-updatesMark H Weaver
2017-08-14gnu: Add bismark....* gnu/packages/bioinformatics.scm (bismark): New variable. Ricardo Wurmus
2017-08-14gnu: Add r-dexseq....* gnu/packages/bioinformatics.scm (r-dexseq): New variable. Ricardo Wurmus
2017-08-09Merge branch 'master' into core-updatesMark H Weaver
2017-08-09gnu: r-wgcna: Update to 1.61....* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61. [propagated-inputs]: Add r-rcpp, r-robust, r-survival. Ricardo Wurmus
2017-08-09gnu: Add reference to (gnu packages graph)....This is a follow-up to 1738138cb3a48ed2f55c59c8d7c6ce12a4c4dcb3. Ricardo Wurmus
2017-08-07Merge branch 'master' into core-updatesMark H Weaver
2017-08-07gnu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash....* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]: Restore hash from before the tarball changed in place. It changed back. This reverts commit fd4085793818ab2aea28dfeeb2728f6f02416c4c. Tobias Geerinckx-Rice
2017-08-06Merge branch 'master' into core-updatesMark H Weaver
2017-08-05gnu: perl: Work around more "dotless @INC" build issues....* gnu/packages/web.scm (perl-www-curl)[arguments]: Add 'set-search-path' phase. * gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Augment 'configure' phase to set PERL5LIB. * gnu/packages/image.scm (steghide)[arguments]: Add #:phases argument. Ludovic Courtès
2017-08-03gnu: bioinformatics.scm: Use (gnu packages cran) module....This is a follow up to a8cba9dd112528d67a946eee057c838221eb5249. * gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules. Efraim Flashner
2017-08-03gnu: r-seqminer: Update to 6.0....* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0. Ricardo Wurmus
2017-08-03gnu: r-wgcna: Update to 1.60....* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60. Ricardo Wurmus
2017-08-03gnu: r-qtl: Update to 1.41-6....* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6. Ricardo Wurmus
2017-08-03gnu: r-seqinr: Update to 3.4-5....* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5. Ricardo Wurmus
2017-08-03gnu: r-optparse: Update to 1.4.4....* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4. Ricardo Wurmus
2017-08-03gnu: r-bookdown: Update to 0.4....* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4. Ricardo Wurmus
2017-08-03gnu: htseq: Use PyPI URI....This is a follow-up to 92971d68ac942cd4a38092b4ccb20a8192a56aaf. * gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'. Ben Woodcroft
2017-08-03gnu: htseq: Update to 0.9.1....* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1. [arguments]: Use python-3 by removing field. [native-inputs]: Add 'python-cython'. [propagated-inputs]: Use python3 numpy package. [inputs]: Use python3 pysam package. Add 'python-matplotlib'. (python2-htseq): New variable. (clipper)[inputs]: Use it. Ben Woodcroft
2017-08-02gnu: r-deseq2: Update to 1.16.1....* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1. Roel Janssen
2017-08-02gnu: r-annotationforge: Update to 1.18.1....* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1. Roel Janssen
2017-08-02gnu: r-category: Update to 2.42.1....* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1. Roel Janssen
2017-08-02gnu: r-biocstyle: Update to 2.4.1....* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1. Roel Janssen
2017-08-02gnu: r-dnacopy: Update to 1.50.1....* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1. Roel Janssen
2017-08-02gnu: r-iranges: Update to 2.10.2....* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2. Roel Janssen
2017-08-02gnu: r-genomeinfodb: Update to 1.12.2....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2. Roel Janssen
2017-08-02gnu: r-variantannotation: Update to 1.22.3....* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3. Roel Janssen
2017-08-02gnu: r-limma: Update to 3.32.5....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5. Roel Janssen
2017-08-02gnu: r-biobase: Update to 2.36.2....* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2. Roel Janssen
2017-08-02gnu: r-annotationdbi: Update to 1.38.2....* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2. Roel Janssen
2017-08-02gnu: r-biomart: Update to 2.32.1....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1. Roel Janssen
2017-08-02gnu: r-biocparallel: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1. Roel Janssen
2017-08-02gnu: r-biostrings: Update to 2.44.2....* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2. Roel Janssen
2017-08-02gnu: r-delayedarray: Update to 0.2.7....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7. Roel Janssen
2017-08-02gnu: r-summarizedexperiment: Update to 1.6.3....* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3. Roel Janssen
2017-08-02gnu: r-genomicalignments: Update to 1.12.1....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1. Roel Janssen
2017-08-02gnu: r-rtracklayer: Update to 1.36.4....* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4. Roel Janssen
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