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* gnu: Explicitly refer to 'guile-json-1' when needed.Ludovic Courtès2019-07-25
| | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Change 'guile-json' to 'guile-json-1'. * gnu/packages/ci.scm (cuirass)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (artanis)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (jupyter-guile-kernel)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (guile-mastodon)[inputs]: Likewise. * gnu/packages/mail.scm (mumi)[inputs]: Likewise. * gnu/packages/package-management.scm (guix)[inputs]: Likewise. * gnu/packages/package-management.scm (guix-daemon)[inputs]: Likewise. * gnu/packages/web.scm (hpcguix-web)[inputs]: Likewise.
* gnu: htslib: Propagate zlib.Ricardo Wurmus2019-07-22
| | | | | | | Reported by Vedran Franke <Vedran.Franke@mdc-berlin.de>. * gnu/packages/bioinformatics.scm (htslib)[inputs]: Move zlib from here... [propagated-inputs]: ...to here.
* gnu: Add python-ont-fast5-api.Ricardo Wurmus2019-07-15
| | | | * gnu/packages/bioinformatics.scm (python-ont-fast5-api): New variable.
* gnu: pigx-rnaseq: Update to 0.0.10.Ricardo Wurmus2019-07-13
| | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.10.
* gnu: r-biocinstaller: Remove entirely.Tobias Geerinckx-Rice2019-07-09
| | | | | | | | This follows up on commit 0971f8bd884b6e92b77d9e12030cd58279699183, which led to ‘r-biocmanager: unbound variable’ errors. See <https://lists.gnu.org/archive/html/guix-devel/2019-07/msg00120.html>. * gnu/packages/bioinformatics.scm (r-biocinstaller): Remove variable.
* gnu: Remove r-biocinstaller.Tobias Geerinckx-Rice2019-07-08
| | | | | | | It requires R < 3.6 and is no longer supported. * gnu/packages/bioinformatics.scm (r-biocinstaller): Define as deprecated in favour of r-biocmanager.
* gnu: r-xbioc: Update to 0.1.16-1.6ff0670.Tobias Geerinckx-Rice2019-07-08
| | | | | | | | | This is needed to deprecate r-biocinstaller, which is no longer distributed. * gnu/packages/bioinformatics.scm (r-xbioc): Update to 0.1.16-1.6ff0670. [propagated-inputs]: Replace deprecated r-biocinstaller with r-biocmanager.
* gnu: nanopolish: Update to 0.11.1-1.6331dc4.Ricardo Wurmus2019-07-05
| | | | * gnu/packages/bioinformatics.scm (nanopolish): Update to 0.11.1-1.6331dc4.
* gnu: pigx-rnaseq: Update to 0.0.8.Ricardo Wurmus2019-07-04
| | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.8.
* gnu: r-phangorn: Update to 2.5.5.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.5.
* gnu: r-tximport: Update to 1.12.3.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.3.
* gnu: r-genomicfeatures: Update to 1.36.3.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.3.
* gnu: r-genomicalignments: Update to 1.20.1.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.20.1.
* gnu: r-biomart: Update to 2.40.1.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.1.
* gnu: r-edger: Update to 3.26.5.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.5.
* gnu: r-systempiper: Update to 1.18.2.Ricardo Wurmus2019-06-29
| | | | * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.2.
* gnu: pigx-scrnaseq: Update to 0.0.8.Ricardo Wurmus2019-06-27
| | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.8.
* gnu: khmer: Update to 3.0.0a3.Ricardo Wurmus2019-06-21
| | | | | | | | * gnu/packages/bioinformatics.scm (khmer): Update to 3.0.0a3. [source]: Remove patch; remove seqan in snippet. [inputs]: Add seqan-1. * gnu/packages/patches/khmer-use-libraries.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: pigx-rnaseq: Update to 0.0.7.Ricardo Wurmus2019-06-20
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.7. [inputs]: Add coreutils and sed.
* gnu: ngs-sdk: Update to 2.9.6.Ricardo Wurmus2019-06-20
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.6.
* gnu: sra-tools: Update to 2.9.6.Ricardo Wurmus2019-06-20
| | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.6.
* gnu: ncbi-vdb: Update to 2.9.6.Ricardo Wurmus2019-06-20
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.6. [arguments]: Pass HAVE_HDF5 make flag; add build phase "patch-krypto-flags".
* gnu: Add tbsp.Ricardo Wurmus2019-06-17
| | | | * gnu/packages/bioinformatics.scm (tbsp): New variable.
* gnu: r-seurat: Update to 3.0.2.Ricardo Wurmus2019-06-17
| | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.2.
* gnu: r-tximport: Update to 1.12.1.Ricardo Wurmus2019-06-17
| | | | * gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.1.
* gnu: r-systempiper: Update to 1.18.1.Ricardo Wurmus2019-06-17
| | | | * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.1.
* gnu: Remove r-loomr.Ricardo Wurmus2019-06-14
| | | | | | | The loomR package is actually non-free software according to its author. See https://github.com/mojaveazure/loomR/pull/24. * gnu/packages/bioinformatics.scm (r-loomr): Remove variable.
* gnu: pigx-rnaseq: Update to 0.0.6.Ricardo Wurmus2019-06-12
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.6. [inputs]: Remove bedtools.
* gnu: Add r-psiplot.Ricardo Wurmus2019-06-11
| | | | * gnu/packages/bioinformatics.scm (r-psiplot): New variable.
* gnu: r-msnbase: Update to 2.10.1.Ricardo Wurmus2019-06-09
| | | | * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.10.1.
* gnu: r-iranges: Update to 2.18.1.Ricardo Wurmus2019-06-09
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.1.
* gnu: r-biocviews: Update to 1.52.2.Ricardo Wurmus2019-06-01
| | | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.52.2. [propagated-inputs]: Add r-biocmanager.
* gnu: r-biocviews: Update to 1.52.1.Ricardo Wurmus2019-05-30
| | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.52.1.
* gnu: r-scran: Update to 1.12.1.Ricardo Wurmus2019-05-29
| | | | * gnu/packages/bioinformatics.scm (r-scran): Update to 1.12.1.
* gnu: r-scater: Update to 1.12.2.Ricardo Wurmus2019-05-29
| | | | * gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.2.
* gnu: r-sva: Update to 3.32.1.Ricardo Wurmus2019-05-29
| | | | * gnu/packages/bioinformatics.scm (r-sva): Update to 3.32.1.
* gnu: r-genomicfeatures: Update to 1.36.1.Ricardo Wurmus2019-05-29
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.1.
* gnu: r-edger: Update to 3.26.4.Ricardo Wurmus2019-05-29
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.4.
* gnu: r-variantannotation: Update to 1.30.1.Ricardo Wurmus2019-05-29
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.30.1.
* gnu: pigx-chipseq: Update to 0.0.41.Ricardo Wurmus2019-05-26
| | | | * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.41.
* gnu: Move Sphinx and friends to (gnu packages sphinx).Marius Bakke2019-05-24
| | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/python-xyz.scm (python-sphinxcontrib-websupport, python2-sphinxcontrib-websupport, python-sphinx, python2-sphinx, python-sphinx-gallery, python2-sphinx-gallery, python-sphinx-rtd-theme, python2-sphinx-rtd-theme, python-guzzle-sphinx-theme, python2-guzzle-sphinx-theme, python-sphinxcontrib-newsfeed, python-sphinxcontrib-programoutput, python2-sphinxcontrib-programoutput, python-sphinx-repoze-interface, python2-sphinx-repoze-interface, python-sphinx-cloud-sptheme, python2-sphinx-cloud-sptheme, python-sphinx-alabaster-theme, python2-sphinx-alabaster-theme, python-sphinx-me, python-sphinxcontrib-svg2pdfconverter): Move to ... (gnu): * gnu/packages/sphinx.scm: ... here. New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly. * gnu/packages/admin.scm, gnu/packages/bioinformatics.scm, gnu/packages/calendar.scm, gnu/packages/cluster.scm, gnu/packages/databases.scm, gnu/packages/dav.scm, gnu/packages/disk.scm, gnu/packages/django.scm, gnu/packages/elf.scm, gnu/packages/emacs-xyz.scm, gnu/packages/emulators.scm, gnu/packages/finance.scm, gnu/packages/image.scm, gnu/packages/libffi.scm, gnu/packages/mail.scm, gnu/packages/mpd.scm, gnu/packages/openstack.scm, gnu/packages/pdf.scm, gnu/packages/python-web.scm, gnu/packages/search.scm, gnu/packages/statistics.scm, gnu/packages/storage.scm, gnu/packages/sync.scm, gnu/packages/terminals.scm, gnu/packages/tls.scm, gnu/packages/web.scm: Adjust module imports.
* gnu: salmon: Update to 0.13.1.Ricardo Wurmus2019-05-23
| | | | | | | | | * gnu/packages/bioinformatics.scm (salmon): Update to 0.13.1. [arguments]: Adjust "do-not-look-for-boost" build phase; adjust "prepare-rapmap" phase; adjust "use-system-libraries" phase. [inputs]: Remove bwa, jellyfish, spdlog-for-salmon. [native-inputs]: Add pkg-config. (spdlog-for-salmon, bwa-for-salmon): Remove variables.
* gnu: umi-tools: Fix typo "containing".Vagrant Cascadian2019-05-22
| | | | * gnu/packages/bioinformatics (umi-tools)[description]: Fix typo.
* gnu: r-gage: Fix typo "functions".Vagrant Cascadian2019-05-22
| | | | * gnu/packages/bioinformatics (r-gage)[description]: Fix typo.
* gnu: r-limma: Update to 3.40.2.Ricardo Wurmus2019-05-20
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.2.
* gnu: r-edger: Update to 3.26.3.Ricardo Wurmus2019-05-20
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.3.
* gnu: r-scater: Update to 1.12.1.Ricardo Wurmus2019-05-20
| | | | * gnu/packages/bioinformatics.scm (r-scater): Update to 1.12.1.
* gnu: r-seurat: Update to 3.0.1.Ricardo Wurmus2019-05-20
| | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.1.
* gnu: r-maldiquant: Update to 1.19.3.Ricardo Wurmus2019-05-20
| | | | * gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.3.
* gnu: r-edger: Update to 3.26.1.Ricardo Wurmus2019-05-20
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.1.
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