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36820 Commits

Author SHA1 Message Date
Ricardo Wurmus 7145f4e519
gnu: ritornello: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus e0a8fc85dd
gnu: snap-aligner: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git.
[arguments]: Use INVOKE.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 6236524409
gnu: sortmerna: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 273df99d7d
gnu: vsearch: Fetch source from git. 
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 67caa4b773
gnu: preseq: Update to 2.0.3. 
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 37e285be43
gnu: preseq: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 63f3255e13
gnu: 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[source]: Remove outdated snippet.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.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus 019fcdf20a
gnu: seqtk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus b9d0c3564b
gnu: raxml: Update to 8.2.12. 
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus d9ba126d17
gnu: python2-biom-format: Fix build. 
This is a follow-up to commit 239716fb0b.

* gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify
phases of base package.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus 4715d4af17
gnu: raxml: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus 5e242b02c3
gnu: pyicoteo: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Efraim Flashner b44b1f08f6
gnu: 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.
 2018-11-07 23:16:02 +02:00
Ludovic Courtès ea68b3f652
pull: Add missing monadic 'return'. 
Fixes a regression introduced in
5f7dd092ca 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.
 2018-11-07 21:56:16 +01:00
Ricardo Wurmus 2b773a9273
gnu: sra-tools: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
 2018-11-07 21:41:56 +01:00
Ricardo Wurmus 55698df260
gnu: libgff: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
 2018-11-07 21:41:56 +01:00
Ricardo Wurmus 4257c10ad2
gnu: kentutils: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 1a20bcadf3
gnu: r-seqgl: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus a2b9d6a8d0
gnu: pplacer: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 6052264b56
gnu: minced: Update to 0.3.2. 
* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 9d94ca0ebf
gnu: minced: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus b58d9e4aa2
gnu: metabat: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 5c1f35e71b
gnu: mash: Update to 2.1. 
* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus 497fc04d8f
gnu: mash: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Marius Bakke b31e156161
gnu: fio: Update to 3.11. 
* gnu/packages/benchmark.scm (fio): Update to 3.11.
[source]: Use bz2 compressed tarball.
 2018-11-07 21:09:00 +01:00
Ricardo Wurmus 2dc28391f3
gnu: kaiju: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
 2018-11-07 20:47:22 +01:00
Ricardo Wurmus 6fe323bf2e
gnu: kaiju: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git.
[arguments]: Remove redundant installation step.
 2018-11-07 20:46:36 +01:00
Ricardo Wurmus f0731591a5
gnu: idr: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
 2018-11-07 20:41:58 +01:00
Ricardo Wurmus b8a6230df3
gnu: java-htsjdk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
 2018-11-07 20:36:07 +01:00
Ricardo Wurmus 57be690d91
gnu: hisat2: Use versioned source URL. 
* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
 2018-11-07 20:32:29 +01:00
Ricardo Wurmus c8f02c1dcb
gnu: grit: Update to 2.0.5. 
* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
 2018-11-07 20:30:44 +01:00
Ricardo Wurmus 8d75adbf03
gnu: grit: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
 2018-11-07 20:27:10 +01:00
Ricardo Wurmus 152bebd9e0
gnu: 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".
 2018-11-07 20:26:46 +01:00
Ricardo Wurmus b113f39019
gnu: gemma: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
 2018-11-07 20:26:45 +01:00
Pierre Langlois f09e8abc5e
gnu: 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>
 2018-11-07 14:25:07 -05:00
Ricardo Wurmus 91b71cfbba
gnu: fxtract: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
 2018-11-07 19:55:50 +01:00
Ricardo Wurmus 7ca49ab57a
gnu: ribodiff: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
 2018-11-07 19:48:21 +01:00
Ricardo Wurmus 239716fb0b
gnu: 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.
 2018-11-07 19:47:07 +01:00
Ricardo Wurmus 007a81d5cf
gnu: python-biom-format: Fetch source from git. 
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
 2018-11-07 19:10:36 +01:00
Ricardo Wurmus 383cb7b8e6
gnu: bioawk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
 2018-11-07 19:06:30 +01:00
Ricardo Wurmus 20ee3e8b76
gnu: bedtools-2.18: Fetch sources from stable URL. 
* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
 2018-11-07 18:52:46 +01:00
Ricardo Wurmus 8e58319c45
gnu: bamtools: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
 2018-11-07 18:44:30 +01:00
Ricardo Wurmus 21335fdbec
gnu: ngless: Install links to required tools. 
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
 2018-11-07 17:19:53 +01:00
Ricardo Wurmus fff67cc8a7
gnu: prodigal: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
 2018-11-07 17:19:53 +01:00
Ludovic Courtès dcb45127e0
services: cuirass: Add 'ttl' configuration field. 
* gnu/services/cuirass.scm (<cuirass-configuration>)[ttl]: New field.
(cuirass-shepherd-service): Honor it.
 2018-11-07 16:06:42 +01:00
Ludovic Courtès 08759829cf
gnu: cuirass: Update to 0b40dca. 
* gnu/packages/ci.scm (cuirass): Update to 0b40dca.
 2018-11-07 16:06:42 +01:00
Ludovic Courtès 970c9993f1
linux-initrd: Make sure 'build-initrd' can delete files. 
Fixes <https://bugs.gnu.org/33297>.
Reported by Mark H Weaver <mhw@netris.org>.

This fixes a regression introduced in
72dc64f8f7, which made files read-only.

* gnu/build/linux-initrd.scm (build-initrd): Call 'make-file-writable'
on all the files under contents/.
 2018-11-07 16:06:42 +01:00
Ricardo Wurmus 9255198423
gnu: r-mzr: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 37200dbcc3
gnu: r-rhdf5lib: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0.
[source]: Add snippet to remove bundled binaries.
[arguments]: Replace references to hdf5 with references to hdf5-1.10.
[native-inputs]: Likewise.
[propagated-inputs]: Replace hdf5 with hdf5-1.10.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus 8e48d36f26
gnu: r-hdf5array: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
 2018-11-07 12:27:16 +01:00