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* gnu: sra-tools: Update to 2.9.3.Ricardo Wurmus2018-11-081-14/+2
| | | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3. [arguments]: Remove build phase patch-away-glibc-conflict.
* gnu: plink-ng: Fetch sources from git.Ricardo Wurmus2018-11-081-5/+6
| | | | * gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
* gnu: ncbi-vdb: Update to 2.9.3.Ricardo Wurmus2018-11-081-2/+2
| | | | * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
* gnu: ngs-sdk: Update to 2.9.3.Ricardo Wurmus2018-11-081-2/+2
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
* gnu: ngs-sdk: Use INVOKE.Ricardo Wurmus2018-11-081-3/+4
| | | | | * gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: emboss: Use INVOKE.Ricardo Wurmus2018-11-081-1/+1
| | | | | * gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: taxtastic: Use INVOKE.Ricardo Wurmus2018-11-081-2/+1
| | | | | * gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: sra-tools: Use INVOKE.Ricardo Wurmus2018-11-081-3/+3
| | | | | * gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: muscle: Use INVOKE.Ricardo Wurmus2018-11-081-2/+3
| | | | | * gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: newick-utils: Remove custom autoconf phase.Ricardo Wurmus2018-11-081-5/+0
| | | | * gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
* gnu: mash: Remove custom autoconf phase.Ricardo Wurmus2018-11-081-3/+1
| | | | * gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
* gnu: vsearch: Remove custom autogen phase.Ricardo Wurmus2018-11-081-5/+0
| | | | * gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
* gnu: java-picard-1.113: Use INVOKE.Ricardo Wurmus2018-11-081-17/+19
| | | | | * gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: fraggenescan: Use INVOKE.Ricardo Wurmus2018-11-081-17/+22
| | | | | * gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in build phases and return #T unconditionally.
* gnu: sailfish: Fetch sources from git.Ricardo Wurmus2018-11-081-6/+6
| | | | * gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
* gnu: ngs-sdk: Fetch sources from git.Ricardo Wurmus2018-11-081-10/+9
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
* gnu: ncbi-vdb: Use INVOKE and end phases on #T.Ricardo Wurmus2018-11-081-3/+3
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and unconditionally end phases with #T.
* gnu: ncbi-vdb: Fetch sources from git.Ricardo Wurmus2018-11-081-10/+11
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git. [arguments]: Add phase to make checkout writable.
* gnu: tadbit: Fetch sources from git.Ricardo Wurmus2018-11-081-6/+7
| | | | | * gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git. [version]: Use "2.0.0" instead of "2.0".
* gnu: pspp: Update to 1.2.0.Kei Kebreau2018-11-071-4/+9
| | | | | | * gnu/packages/statistics.scm (pspp): Update to 1.2.0. [inputs]: Add spread-sheet-widget. [native-inputs]: Add autoconf, python-2, and texinfo.
* gnu: Add spread-sheet-widget.Kei Kebreau2018-11-071-0/+27
| | | | * gnu/packages/gtk.scm (spread-sheet-widget): New public variable.
* gnu: filevercmp: Fetch sources from git.Ricardo Wurmus2018-11-071-7/+10
| | | | | * gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git. [arguments]: Add #T to the end of the install phase.
* gnu: ritornello: Update to 2.0.1.Ricardo Wurmus2018-11-071-3/+3
| | | | | * gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1. [arguments]: Adjust file patching.
* gnu: ritornello: Fetch sources from git.Ricardo Wurmus2018-11-071-6/+6
| | | | * gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
* gnu: snap-aligner: Fetch sources from git.Ricardo Wurmus2018-11-071-7/+7
| | | | | * gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git. [arguments]: Use INVOKE.
* gnu: sortmerna: Fetch sources from git.Ricardo Wurmus2018-11-071-6/+6
| | | | * gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
* gnu: vsearch: Fetch source from git.Ricardo Wurmus2018-11-071-6/+6
| | | | * gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
* gnu: preseq: Update to 2.0.3.Ricardo Wurmus2018-11-071-7/+6
| | | | * gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
* gnu: preseq: Fetch sources from git.Ricardo Wurmus2018-11-071-5/+6
| | | | * gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
* gnu: seqtk: Update to 1.3.Ricardo Wurmus2018-11-071-12/+5
| | | | | | * gnu/packages/bioinformatics.scm (seqtk): Update to 1.3. [source]: Remove outdated snippet. [arguments]: Use INVOKE and return #T unconditionally.
* gnu: seqtk: Fetch sources from git.Ricardo Wurmus2018-11-071-7/+7
| | | | * gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
* gnu: raxml: Update to 8.2.12.Ricardo Wurmus2018-11-071-2/+2
| | | | * gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
* gnu: python2-biom-format: Fix build.Ricardo Wurmus2018-11-071-9/+9
| | | | | | | This is a follow-up to commit 239716fb0ba0a7cd81f9d59dcf5a2261b8efe4fa. * gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify phases of base package.
* gnu: raxml: Fetch sources from git.Ricardo Wurmus2018-11-071-7/+6
| | | | * gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
* gnu: pyicoteo: Fetch sources from git.Ricardo Wurmus2018-11-071-5/+6
| | | | * gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
* gnu: hplip: Remove bundled non-free blobs.Efraim Flashner2018-11-073-1/+238
| | | | | | | | | 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.
* gnu: sra-tools: Fetch sources from git.Ricardo Wurmus2018-11-071-6/+6
| | | | * gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
* gnu: libgff: Fetch sources from git.Ricardo Wurmus2018-11-071-6/+6
| | | | * gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
* gnu: kentutils: Fetch sources from git.Ricardo Wurmus2018-11-071-5/+8
| | | | | * gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git. [arguments]: Add phase "fix-permissions".
* gnu: r-seqgl: Fetch sources from git.Ricardo Wurmus2018-11-071-5/+6
| | | | * gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
* gnu: pplacer: Fetch sources from git.Ricardo Wurmus2018-11-071-7/+9
| | | | | * gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git. [arguments]: Make files writable; use INVOKE.
* gnu: minced: Update to 0.3.2.Ricardo Wurmus2018-11-071-2/+2
| | | | * gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
* gnu: minced: Fetch sources from git.Ricardo Wurmus2018-11-071-6/+6
| | | | * gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
* gnu: metabat: Fetch sources from git.Ricardo Wurmus2018-11-071-5/+6
| | | | * gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
* gnu: mash: Update to 2.1.Ricardo Wurmus2018-11-071-2/+2
| | | | * gnu/packages/bioinformatics.scm (mash): Update to 2.1.
* gnu: mash: Fetch sources from git.Ricardo Wurmus2018-11-071-6/+6
| | | | * gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
* gnu: fio: Update to 3.11.Marius Bakke2018-11-071-3/+3
| | | | | * gnu/packages/benchmark.scm (fio): Update to 3.11. [source]: Use bz2 compressed tarball.
* gnu: kaiju: Update to 1.6.3.Ricardo Wurmus2018-11-071-2/+2
| | | | * gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
* gnu: kaiju: Fetch sources from git.Ricardo Wurmus2018-11-071-8/+7
| | | | | * gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git. [arguments]: Remove redundant installation step.
* gnu: idr: Fetch sources from git.Ricardo Wurmus2018-11-071-6/+6
| | | | * gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
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