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* gnu: ngs-sdk: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: emboss: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: taxtastic: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: sra-tools: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: muscle: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: newick-utils: Remove custom autoconf phase.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
* gnu: mash: Remove custom autoconf phase.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
* gnu: vsearch: Remove custom autogen phase.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
* gnu: java-picard-1.113: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: fraggenescan: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in build phases and return #T unconditionally.
* gnu: sailfish: Fetch sources from git.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
* gnu: ngs-sdk: Fetch sources from git.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
* gnu: ncbi-vdb: Use INVOKE and end phases on #T.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and unconditionally end phases with #T.
* gnu: ncbi-vdb: Fetch sources from git.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git. [arguments]: Add phase to make checkout writable.
* gnu: tadbit: Fetch sources from git.Ricardo Wurmus2018-11-08
| | | | | * 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 Kebreau2018-11-07
| | | | | | * 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 Kebreau2018-11-07
| | | | * gnu/packages/gtk.scm (spread-sheet-widget): New public variable.
* gnu: filevercmp: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | | * 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 Wurmus2018-11-07
| | | | | * gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1. [arguments]: Adjust file patching.
* gnu: ritornello: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
* gnu: snap-aligner: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | | * gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git. [arguments]: Use INVOKE.
* gnu: sortmerna: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
* gnu: vsearch: Fetch source from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
* gnu: preseq: Update to 2.0.3.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
* gnu: preseq: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
* gnu: seqtk: Update to 1.3.Ricardo Wurmus2018-11-07
| | | | | | * 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 Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
* gnu: raxml: Update to 8.2.12.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
* gnu: python2-biom-format: Fix build.Ricardo Wurmus2018-11-07
| | | | | | | 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 Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
* gnu: pyicoteo: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
* gnu: hplip: Remove bundled non-free blobs.Efraim Flashner2018-11-07
| | | | | | | | | 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.
* pull: Add missing monadic 'return'.Ludovic Courtès2018-11-07
| | | | | | | | | | | | | | | | | | | | | | | Fixes a regression introduced in 5f7dd092ca577a534067f577b8849ed06cabf970 where, upon completion, 'guix pull' would fail (instead of printing the new/upgraded packages) with ugly errors like: successfully built /gnu/store/…-profile.drv 1 package in profile Backtrace: […] In guix/store.scm: 1605:24 1 (run-with-store _ _ #:guile-for-build _ #:system _ # _) In unknown file: 0 (_ #<build-daemon 256.97 2476b40>) ERROR: Wrong type to apply: #t Reported by thorwil on #guix. * guix/scripts/pull.scm (build-and-install): Add missing 'return' when DRY-RUN? is wrong.
* gnu: sra-tools: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
* gnu: libgff: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
* gnu: kentutils: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | | * gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git. [arguments]: Add phase "fix-permissions".
* gnu: r-seqgl: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
* gnu: pplacer: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | | * gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git. [arguments]: Make files writable; use INVOKE.
* gnu: minced: Update to 0.3.2.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
* gnu: minced: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
* gnu: metabat: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
* gnu: mash: Update to 2.1.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (mash): Update to 2.1.
* gnu: mash: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
* gnu: fio: Update to 3.11.Marius Bakke2018-11-07
| | | | | * gnu/packages/benchmark.scm (fio): Update to 3.11. [source]: Use bz2 compressed tarball.
* gnu: kaiju: Update to 1.6.3.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
* gnu: kaiju: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | | * gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git. [arguments]: Remove redundant installation step.
* gnu: idr: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
* gnu: java-htsjdk: Fetch sources from git.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
* gnu: hisat2: Use versioned source URL.Ricardo Wurmus2018-11-07
| | | | * gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
* gnu: grit: Update to 2.0.5.Ricardo Wurmus2018-11-07
| | | | | * gnu/packages/bioinformatics.scm (grit): Update to 2.0.5. [arguments]: Simplify.
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