Ricardo Wurmus
e78e54d029
gnu: emboss: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:14:09 +01:00
Ricardo Wurmus
8b685c4720
gnu: taxtastic: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:13:35 +01:00
Ricardo Wurmus
2e2d88539c
gnu: sra-tools: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:12:43 +01:00
Ricardo Wurmus
179416467f
gnu: muscle: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:11:38 +01:00
Ricardo Wurmus
0881d62f25
gnu: newick-utils: Remove custom autoconf phase.
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* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
2018-11-08 09:10:58 +01:00
Ricardo Wurmus
e35dce0170
gnu: mash: Remove custom autoconf phase.
...
* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
2018-11-08 09:10:20 +01:00
Ricardo Wurmus
31c41a8cfe
gnu: vsearch: Remove custom autogen phase.
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* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
2018-11-08 09:04:34 +01:00
Ricardo Wurmus
c527d36f02
gnu: java-picard-1.113: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
2018-11-08 09:02:34 +01:00
Ricardo Wurmus
e438c96558
gnu: fraggenescan: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
2018-11-08 08:58:46 +01:00
Ricardo Wurmus
c098c49b3e
gnu: sailfish: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
2018-11-08 08:53:54 +01:00
Ricardo Wurmus
4031e7f1ec
gnu: ngs-sdk: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
2018-11-08 08:53:53 +01:00
Ricardo Wurmus
6a7d9ee39f
gnu: ncbi-vdb: Use INVOKE and end phases on #T.
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* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and
unconditionally end phases with #T.
2018-11-08 08:53:53 +01:00
Ricardo Wurmus
3398dfb764
gnu: ncbi-vdb: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git.
[arguments]: Add phase to make checkout writable.
2018-11-08 08:53:53 +01:00
Ricardo Wurmus
e0f1aa2d2b
gnu: tadbit: Fetch sources from git.
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* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git.
[version]: Use "2.0.0" instead of "2.0".
2018-11-08 08:53:50 +01:00
Kei Kebreau
ed33049cdc
gnu: pspp: Update to 1.2.0.
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* gnu/packages/statistics.scm (pspp): Update to 1.2.0.
[inputs]: Add spread-sheet-widget.
[native-inputs]: Add autoconf, python-2, and texinfo.
2018-11-07 17:46:25 -05:00
Kei Kebreau
e2f36385d3
gnu: Add spread-sheet-widget.
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* gnu/packages/gtk.scm (spread-sheet-widget): New public variable.
2018-11-07 17:46:25 -05:00
Ricardo Wurmus
f3f34b132c
gnu: filevercmp: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git.
[arguments]: Add #T to the end of the install phase.
2018-11-07 23:17:36 +01:00
Ricardo Wurmus
3b888065da
gnu: ritornello: Update to 2.0.1.
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* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1.
[arguments]: Adjust file patching.
2018-11-07 23:17:36 +01:00
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.
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* 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.
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* 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.
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* 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.
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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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
Marius Bakke
55174e668f
Merge branch 'master' into core-updates
2018-11-07 21:09:57 +01:00
Marius Bakke
b31e156161
gnu: fio: Update to 3.11.
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* gnu/packages/benchmark.scm (fio): Update to 3.11.
[source]: Use bz2 compressed tarball.
2018-11-07 21:09:00 +01:00
Marius Bakke
1badc85068
gnu: ceph: Update to 13.2.2.
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* 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.
2018-11-07 21:01:12 +01:00
Ricardo Wurmus
2dc28391f3
gnu: kaiju: Update to 1.6.3.
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* 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.
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* 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.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
2018-11-07 20:32:29 +01:00