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2018-11-08gnu: java-picard-1.113: Use INVOKE.•••* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus
2018-11-08gnu: fraggenescan: Use INVOKE.•••* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in build phases and return #T unconditionally. Ricardo Wurmus
2018-11-08gnu: sailfish: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git. Ricardo Wurmus
2018-11-08gnu: ngs-sdk: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git. Ricardo Wurmus
2018-11-08gnu: ncbi-vdb: Use INVOKE and end phases on #T.•••* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and unconditionally end phases with #T. Ricardo Wurmus
2018-11-08gnu: ncbi-vdb: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git. [arguments]: Add phase to make checkout writable. Ricardo Wurmus
2018-11-08gnu: tadbit: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git. [version]: Use "2.0.0" instead of "2.0". Ricardo Wurmus
2018-11-07gnu: pspp: Update to 1.2.0.•••* gnu/packages/statistics.scm (pspp): Update to 1.2.0. [inputs]: Add spread-sheet-widget. [native-inputs]: Add autoconf, python-2, and texinfo. Kei Kebreau
2018-11-07gnu: Add spread-sheet-widget.•••* gnu/packages/gtk.scm (spread-sheet-widget): New public variable. Kei Kebreau
2018-11-07gnu: filevercmp: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git. [arguments]: Add #T to the end of the install phase. Ricardo Wurmus
2018-11-07gnu: ritornello: Update to 2.0.1.•••* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1. [arguments]: Adjust file patching. Ricardo Wurmus
2018-11-07gnu: ritornello: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: snap-aligner: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git. [arguments]: Use INVOKE. Ricardo Wurmus
2018-11-07gnu: sortmerna: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: vsearch: Fetch source from git.•••* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: preseq: Update to 2.0.3.•••* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3. Ricardo Wurmus
2018-11-07gnu: preseq: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: seqtk: Update to 1.3.•••* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3. [source]: Remove outdated snippet. [arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus
2018-11-07gnu: seqtk: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: raxml: Update to 8.2.12.•••* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12. Ricardo Wurmus
2018-11-07gnu: python2-biom-format: Fix build.•••This is a follow-up to commit 239716fb0ba0a7cd81f9d59dcf5a2261b8efe4fa. * gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify phases of base package. Ricardo Wurmus
2018-11-07gnu: raxml: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: pyicoteo: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: hplip: Remove bundled non-free blobs.•••This fixes <https://bugs.gnu.org/32184>. * gnu/packages/cups.scm (hplip)[source]: Add patch. Update snippet to remove non-free code and binary blobs. * gnu/packages/patches/hplip-remove-imageprocessor.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. Efraim Flashner
2018-11-07gnu: sra-tools: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: libgff: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: kentutils: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git. [arguments]: Add phase "fix-permissions". Ricardo Wurmus
2018-11-07gnu: r-seqgl: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: pplacer: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git. [arguments]: Make files writable; use INVOKE. Ricardo Wurmus
2018-11-07gnu: minced: Update to 0.3.2.•••* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2. Ricardo Wurmus
2018-11-07gnu: minced: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: metabat: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: mash: Update to 2.1.•••* gnu/packages/bioinformatics.scm (mash): Update to 2.1. Ricardo Wurmus
2018-11-07gnu: mash: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git. Ricardo Wurmus
2018-11-07Merge branch 'master' into core-updatesMarius Bakke
2018-11-07gnu: fio: Update to 3.11.•••* gnu/packages/benchmark.scm (fio): Update to 3.11. [source]: Use bz2 compressed tarball. Marius Bakke
2018-11-07gnu: ceph: Update to 13.2.2.•••* gnu/packages/patches/ceph-skip-unittest_blockdev.patch: Adjust for 13.2.2. * gnu/packages/patches/ceph-rocksdb-compat.patch: Delete file. * gnu/packages/patches/ceph-detect-rocksdb.patch, gnu/packages/patches/ceph-volume-respect-PATH.patch: New files. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/storage.scm (ceph): Update to 13.2.2. [source]: Don't remove src/dpdk, which has been moved to src/spdk/dpdk and is purged elsewhere. Drop bundled rapidjson. Adjust patch list. [arguments]: Add "-DWITH_MGR_DASHBOARD_FRONTEND=OFF" and "-DWITH_SPDK=OFF" to #:configure-flags. Drop obsolete "-DWITH_EMBEDDED". Add workaround for <https://bugs.gnu.org/30756>. Remove obsolete test substitution. Rework 'wrap-python-script' to be less verbose and wrap more scripts. [native-inputs]: Add GCC-7. [inputs]: Add OATH-TOOLKIT, RAPIDJSON and PYTHON2-SIX. Marius Bakke
2018-11-07gnu: kaiju: Update to 1.6.3.•••* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3. Ricardo Wurmus
2018-11-07gnu: kaiju: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git. [arguments]: Remove redundant installation step. Ricardo Wurmus
2018-11-07gnu: idr: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: java-htsjdk: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: hisat2: Use versioned source URL.•••* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL. Ricardo Wurmus
2018-11-07gnu: grit: Update to 2.0.5.•••* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5. [arguments]: Simplify. Ricardo Wurmus
2018-11-07gnu: grit: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: gemma: Update to 0.98.•••* gnu/local.mk (dist_patch_DATA): Remove patch. * gnu/packages/patches/gemma-intel-compat.patch: Remove file. * gnu/packages/bioinformatics.scm (gemma): Update to 0.98. [source]: Remove patch. [inputs]: Add eigen, gfortran:lib, and openblas. [arguments]: Add phase "find-eigen". Ricardo Wurmus
2018-11-07gnu: gemma: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: clementine: Build with sqlite-with-column-metadata.•••* gnu/packages/music.scm (clementine)[inputs]: Use sqlite-with-column-metadata. Signed-off-by: Leo Famulari <leo@famulari.name> Pierre Langlois
2018-11-07gnu: fxtract: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: ribodiff: Fetch sources from git.•••* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git. Ricardo Wurmus
2018-11-07gnu: python-biom-format: Update to 2.1.7.•••* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7. [arguments]: Add phases "use-cython", "disable-broken-test", and "make-files-writable". [propagated-inputs]: Add python-flake8. [native-inputs]: Add python-cython, python-pytest, and python-pytest-cov. Ricardo Wurmus
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