96c4621056
gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
...
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-29 01:25:08 +02:00
f7283db37d
gnu: Add BioPerl.
...
* gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.
2015-08-26 17:54:52 +02:00
c1670a8196
gnu: shogun: Move package to machine-learning.scm.
...
* gnu/packages/bioinformatics.scm (shogun): Move from here...
* gnu/packages/machine-learning.scm (shogun): ...to here.
2015-08-14 17:17:05 +02:00
b81cb1f2f3
gnu: bedtools: Add patch to fix compilation on 32 bit systems.
...
* gnu/packages/patches/bedtools-32bit-compilation.patch: New file.
* gnu/packages/bioinformatics.scm (bedtools)[source]: Add patch.
* gnu-system.am (dist_patch_DATA): Register patch.
Signed-off-by: Andreas Enge <andreas@enge.fr>
2015-07-25 19:16:49 +02:00
bd4af2f940
gnu: bedtools: Update to 2.24.0.
...
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.
2015-07-25 00:02:54 -04:00
8dc797fa28
gnu: Add aragorn.
...
* gnu/packages/bioinformatics.scm (aragorn): New variable.
2015-07-21 16:39:38 +02:00
5ede5f2f1c
gnu: metabat: Minor tweaks.
...
* gnu/packages/bioinformatics.scm (metabat)[arguments]: Fix indentation in
'fix-includes' phase.
[license]: Fix misspelling.
2015-07-19 15:27:15 -04:00
8fd790eb87
gnu: Add metabat.
...
* gnu/packages/bioinformatics.scm (metabat): New variable.
2015-07-19 15:17:08 -04:00
9f04196d88
gnu: preseq: Move "use-samtools-headers" phase.
...
* gnu/packages/bioinformatics.scm (preseq)[arguments]: Move phase
"use-samtools-headers" after "enter-dir" phase.
2015-07-09 12:12:07 +02:00
56e373ef75
gnu: Add preseq.
...
* gnu/packages/bioinformatics.scm (preseq): New variable.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: New file.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: New file.
* gnu-system.am (dist_patch_DATA): Add them.
2015-07-08 17:05:00 +02:00
5bdda30b32
gnu: samtools: Install headers.
...
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
"install-headers" to install header files.
2015-07-08 17:05:00 +02:00
795c01f31d
gnu: samtools: Update to 1.2.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.2.
2015-07-07 14:43:07 +02:00
af86047537
gnu: Add prodigal.
...
* gnu/packages/bioinformatics.scm (prodigal): New variable.
2015-07-05 02:56:53 -04:00
151714ca8c
gnu: shogun: Build with install RPATH.
...
* gnu/packages/bioinformatics.scm (shogun)[arguments]: Add configure flag to
build with install RPATH.
2015-07-04 17:55:30 +02:00
c61fe02cc0
gnu: Add WarpedLMM.
...
* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
2015-07-02 11:16:46 +02:00
82c370dea1
gnu: Add Blast+.
...
* gnu/packages/bioinformatics.scm (blast+): New variable.
2015-06-29 16:13:28 +02:00
cc6ed47737
gnu: Add plink.
...
* gnu/packages/bioinformatics.scm (plink): New variable.
* gnu/packages/patches/plink-1.07-unclobber-i.patch: New file.
2015-06-29 12:54:48 +02:00
c684629f7c
gnu: Add hmmer.
...
* gnu/packages/bioinformatics.scm (hmmer): New variable.
2015-06-24 00:39:22 -04:00
4758eaaa2d
gnu: star: Update to 2.4.2a.
...
* gnu/packages/bioinformatics.scm (star): Update to 2.4.2a.
2015-06-23 18:37:16 +02:00
0ec8b206d4
gnu: miso: Install executables.
...
* gnu/packages/bioinformatics.scm (miso)[source]: Patch "setup.py" to use
"setuptools" so that executables are built.
* gnu/packages/bioinformatics.scm (miso)[native-inputs]: Add "python2-mock"
and "python2-pytz".
2015-06-23 13:13:03 +02:00
c4325f6269
gnu: Add idr.
...
* gnu/packages/bioinformatics.scm (idr): New variable.
2015-06-23 10:55:52 +02:00
12b04cbee6
gnu: Add fasttree.
...
* gnu/packages/bioinformatics.scm (fasttree): New variable.
2015-06-21 03:30:40 -04:00
684bf7c7f1
gnu: Add diamond.
...
* gnu/packages/bioinformatics.scm (diamond): New variable.
2015-06-17 19:43:54 -04:00
86517de69c
gnu: miso: Use HTTPS URL.
...
* gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for
downloading the source tarball.
2015-06-17 15:28:43 +02:00
1bbc3b1d2c
gnu: bedops: Update to 2.4.14.
...
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.14.
2015-06-17 14:37:29 +02:00
a98c6eccf8
gnu: orfm: Update to 0.4.1.
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* gnu/packages/bioinformatics.scm (orfm): Update to 0.4.1.
2015-06-15 10:36:42 +02:00
1e44cf8b0f
gnu: Add OrfM.
...
* gnu/packages/bioinformatics.scm (orfm): New variable.
Signed-off-by: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
2015-06-12 12:57:30 +02:00
36742f4389
gnu: Add Couger.
...
* gnu/packages/bioinformatics.scm (couger): New variable.
2015-06-12 12:57:30 +02:00
e0a02cb21f
gnu: ngs-sdk: Update to version 1.1.1.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to version 1.1.1.
2015-06-12 12:57:29 +02:00
e7c097306d
gnu: Add HTSlib.
...
* gnu/packages/bioinformatics.scm (htslib): New variable.
2015-06-02 14:30:14 +02:00
132b4c8c23
gnu: ncbi-vdb: Use "i386" instead of "i686" in directory name.
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* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Copy libraries from
"linux/gcc/i386" directory instead of "linux/gcc/i686" when building on
i686.
2015-06-02 14:26:14 +02:00
365c815389
gnu: Add edirect.
...
* gnu/packages/bioinformatics.scm (edirect): New variable.
2015-05-27 17:42:40 +02:00
628bd9b8a7
gnu: shogun: Remove non-free source files.
...
* gnu/packages/bioinformatics.scm (shogun)[source]: Add snippet to remove
non-free sources.
2015-05-27 10:56:27 +02:00
66e3eff1e3
gnu: Add rsem.
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* gnu/packages/bioinformatics.scm (rsem): New variable.
* gnu/packages/patches/rsem-makefile.patch: New file.
2015-05-22 13:14:29 +02:00
7c3958e15a
gnu: vcftools: Remove "-m64" from CFLAGS.
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* gnu/packages/bioinformatics.scm (vcftools): Explicitly set CFLAGS to
remove "-m64" flag.
2015-05-05 10:20:21 +02:00
4702cec246
gnu: bamtools: Set rpath via LDFLAGS.
...
* gnu/packages/bioinformatics.scm (bamtools): Add a pre-configure phase
setting $LDFLAGS to set the rpath to $out/lib/bamtools.
2015-05-04 11:29:41 +02:00
0b84a0aaca
gnu: Add samtools-0.1.19.
...
* gnu/packages/bioinformatics.scm (samtools-0.1): New variable.
2015-05-04 10:28:27 +02:00
41dd712657
gnu: samtools: Install libbam.a library.
...
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
"install-library" to install the libbam.a library.
2015-05-04 10:28:26 +02:00
0a75450c14
gnu: samtools: Remove patch-makefile-curses phase.
...
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Remove
patch-makefile-curses phase, use make-flags instead.
2015-05-04 10:28:26 +02:00
4ca009c036
gnu: flexbar: Enable tests.
...
* gnu/packages/bioinformatics.scm (flexbar): Enable tests.
2015-04-27 15:12:47 +02:00
e4e5a4d88f
gnu: Add eXpress.
...
* gnu/packages/bioinformatics.scm (express): New variable.
2015-04-21 17:57:22 +02:00
9794180d5e
gnu: Add bamtools.
...
* gnu/packages/bioinformatics.scm (bamtools): New variable.
2015-04-21 17:57:22 +02:00
dbf4ed7c91
gnu: Add subread.
...
* gnu/packages/bioinformatics.scm (subread): New variable.
2015-04-21 10:46:23 +02:00
51c649992e
gnu: Add sra-tools.
...
* gnu/packages/bioinformatics.scm (sra-tools): New variable.
2015-04-20 15:29:17 +02:00
75dd242480
gnu: Add NCBI VDB.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb): New variable.
2015-04-20 15:29:17 +02:00
2651a5e695
gnu: Add NGS Java bindings.
...
* gnu/packages/bioinformatics.scm (ngs-java): New variable.
2015-04-20 15:29:16 +02:00
282c5087b4
gnu: Add NGS SDK.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): New variable.
2015-04-20 15:28:58 +02:00
85c37e29a4
gnu: Add Biopython.
...
* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New
variables.
2015-04-20 15:23:23 +02:00
2127cedb23
gnu: Add FASTX Toolkit.
...
* gnu/packages/bioinformatics.scm (fastx-toolkit): New variable.
2015-04-16 10:28:37 +02:00
8214b7fbea
gnu: rseqc: Update hash.
...
* gnu/packages/bioinformatics.scm (rseqc): Update hash.
2015-04-13 15:39:02 +02:00
5854f6858b
gnu: Add GRIT.
...
* gnu/packages/bioinformatics.scm (grit): New variable.
2015-04-10 14:35:48 +02:00
c833ab556f
gnu: Add Shogun.
...
* gnu/packages/bioinformatics.scm (shogun): New variable.
2015-04-09 15:05:12 +02:00
bfe3c68572
gnu: Add clustal omega.
...
* gnu/packages/bioinformatics.scm (clustal-omega): New variable.
2015-04-01 11:39:39 +02:00
c5372108f2
gnu: pbtranscript-tofu: Add missing inputs.
...
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[inputs]: Add missing
runtime inputs.
2015-03-31 20:04:41 +02:00
49261e45d8
gnu: pbtranscript-tofu: Delete pre-built libraries.
...
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Delete
"build" directory and any shared objects after unpacking.
2015-03-31 20:04:32 +02:00
de07c0db4a
gnu: Add vcftools.
...
* gnu/packages/bioinformatics.scm (vcftools): New variable.
2015-03-31 17:43:52 +02:00
8e913213d9
gnu: Add cutadapt.
...
* gnu/packages/bioinformatics.scm (cutadapt): New variable.
2015-03-31 17:38:56 +02:00
2c16316ef4
gnu: Add pbtranscript-tofu.
...
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable.
2015-03-24 16:59:47 +01:00
ad641d53de
gnu: Add python2-bx-python.
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* gnu/packages/bioinformatics.scm (python2-bx-python): New variable.
2015-03-24 15:00:09 +01:00
19ee920144
gnu: Add python2-pbcore.
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* gnu/packages/bioinformatics.scm (python2-pbcore): New variable.
2015-03-24 14:58:47 +01:00
ddd82e0e76
gnu: Add MISO.
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* gnu/packages/bioinformatics.scm (miso): New variable.
2015-03-17 12:29:58 +01:00
9a8336d87b
gnu: Add bwa.
...
* gnu/packages/bioinformatics.scm (bwa): New variable.
2015-03-17 12:29:51 +01:00
15a3c3d4f1
gnu: Add htsjdk.
...
* gnu/packages/bioinformatics.scm (htsjdk): New variable.
2015-03-10 11:46:49 +01:00
1289062522
Merge branch 'core-updates'.
2015-03-04 14:07:23 +01:00
191c710139
gnu: Add crossmap.
...
* gnu/packages/bioinformatics.scm (crossmap): New variable.
* gnu/packages/patches/crossmap-allow-system-pysam.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
2015-03-02 17:23:56 +01:00
810cff8557
gnu: Add CLIPper.
...
* gnu/packages/bioinformatics.scm (clipper): New variable.
2015-03-02 14:11:54 +01:00
d57e6d0f8e
gnu: Add MACS.
...
* gnu/packages/bioinformatics.scm (macs): New variable.
2015-03-02 11:33:13 +01:00
a2fb1492af
gnu: Add pybedtools.
...
* gnu/packages/bioinformatics.scm (python2-pybedtools): New variable.
2015-03-02 11:32:10 +01:00
f586c87705
gnu: Add 'file-name' fields for github source tarballs without a name.
...
* gnu/packages/aarddict.scm (aarddict), gnu/packages/algebra.scm (arb),
gnu/packages/audio.scm (jack-2, lvtk),
gnu/packages/bioinformatics.scm (bedops, bedtools, bowtie),
gnu/packages/game-development.scm (tiled),
gnu/packages/games.scm (minetest-data, minetest, retroarch),
gnu/packages/jrnl.scm (jrnl), gnu/packages/kde.scm (qjson),
gnu/packages/libevent.scm (libuv), gnu/packages/linux.scm (pflask),
gnu/packages/mail.scm (offlineimap, libetpan),
gnu/packages/maths.scm (arpack-ng), gnu/packages/ninja.scm (ninja),
gnu/packages/nutrition.scm (gourmet),
gnu/packages/python.scm (python-cairocffi), gnu/packages/rdf.scm (lrdf),
gnu/packages/ruby.scm (ruby-i18n), gnu/packages/sxiv.scm (sxiv): Add
'file-name' field to origin.
2015-02-28 09:49:01 -05:00
da6dd842d0
gnu: Remove now unneeded 'unpack' phases for unzip.
...
This is a followup to commit cd0385b
2015-02-27 15:08:37 +01:00
85652f599a
gnu: Add HTSeq.
...
* gnu/packages/bioinformatics.scm (htseq): New variable.
2015-02-20 19:31:53 +01:00
8622a07280
gnu: Add RSeQC.
...
* gnu/packages/bioinformatics.scm (rseqc): New variable.
2015-02-19 13:41:38 +01:00
8dd4ff1133
gnu: Add bedops.
...
* gnu/packages/bioinformatics.scm (bedops): New variable.
2015-02-13 15:51:10 +01:00
e58d01faf5
gnu: hisat: fix build on non-x86_64.
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* gnu/packages/bioinformatics.scm (hisat): Add "POPCNT_CAPABILITY=0" to
make-flags on architectures other than x86_64.
2015-02-12 14:09:00 +01:00
ce7155d5dd
gnu: Add STAR.
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* gnu/packages/bioinformatics.scm (star): New variable.
2015-02-10 14:37:14 +01:00
346a829a85
gnu: Add HISAT.
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* gnu/packages/bioinformatics.scm (hisat): New variable.
2015-02-10 14:37:13 +01:00
d7678942f9
gnu: Add flexbar.
...
* gnu/packages/bioinformatics.scm (flexbar): New variable.
2015-02-09 10:26:28 +01:00
d3517eda25
gnu: Add seqan.
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* gnu/packages/bioinformatics.scm (seqan): New variable.
2015-02-09 10:26:20 +01:00
241e122193
gnu: bowtie: fix build errors
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* gnu/packages/bioinformatics.scm (bowtie): Add 'supported-systems' field and
add Makefile patch.
* gnu/packages/patches/bowtie-fix-makefile.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
2015-01-30 10:45:27 +01:00
2c7ee16720
gnu: Add bowtie
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* gnu/packages/bioinformatics.scm (bowtie): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-19 18:50:28 +01:00
81de56479a
gnu: Add bedtools
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* gnu/packages/bioinformatics.scm (bedtools): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-16 18:17:15 +01:00
f3cd952b45
gnu: samtools: disable tests for non-64-bit systems
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* gnu/packages/bioinformatics.scm (samtools): disable tests for all non-64-bit
systems because of an upstream bug in the test data.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-16 18:17:15 +01:00
4e10a22168
gnu: Add samtools
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* gnu/packages/bioinformatics.scm: New file
* gnu-system.am (GNU_SYSTEM_MODULES): Add it
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-13 00:01:06 +01:00
Ludovic Courtès