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.
...
* 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.
...
* 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.
...
* 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.
...
* 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
Ludovic Courtès
Ricardo Wurmus
Ben Woodcroft
Mark H Weaver
Ricardo Wurmus
Ben Woodcroft