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2311 commits

Author SHA1 Message Date
Ricardo Wurmus
9dc50c8c47
gnu: sra-tools: Update to 2.10.6. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.10.6.
[arguments]: Replace CC variable in utf8proc Makefile.
[inputs]: Replace hdf5 with hdf5-1.10; add python-wrapper.
 2020-05-19 12:42:01 +02:00
Ricardo Wurmus
68de995674
gnu: ncbi-vdb: Update to 2.10.6. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.10.6.
 2020-05-19 12:42:01 +02:00
Ricardo Wurmus
6437c598e7
gnu: ngs-sdk: Update to 2.10.5. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.10.5.
 2020-05-19 12:42:01 +02:00
Marius Bakke
87a40d7203
Merge branch 'master' into core-updates 2020-05-05 20:43:21 +02:00
Efraim Flashner
31def9a9df
gnu: Add grocsvs. 
* gnu/packages/bioinformatics.scm (grocsvs): New variable.
* gnu/packages/patches/grocsvs-dont-use-admiral.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2020-05-05 10:06:28 +03:00
Marius Bakke
8bf8cd9b85
Merge branch 'master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/backup.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/guile.scm
	gnu/packages/lisp.scm
	gnu/packages/openldap.scm
	gnu/packages/package-management.scm
	gnu/packages/web.scm
	gnu/packages/xorg.scm
 2020-04-30 23:47:49 +02:00
Roel Janssen
eca648b65b
gnu: Add miniasm. 
* gnu/packages/bioinformatics.scm (miniasm): New variable.
 2020-04-30 15:30:16 +02:00
Ricardo Wurmus
4a148c6da3
gnu: python2-warpedlmm: Fix build. 
* gnu/packages/bioinformatics.scm (python2-warpedlmm)[propagated-inputs]: Add
python2-weave.
[arguments]: Disable tests and add "use-weave" phase.
 2020-04-30 13:08:33 +02:00
Ricardo Wurmus
545e12f40d
gnu: Add variant-tools. 
* gnu/packages/bioinformatics.scm (variant-tools): New variable.
 2020-04-28 12:23:28 +02:00
Ricardo Wurmus
9c726c485a
gnu: r-hdf5array: Update to 1.14.4. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.4.
 2020-04-28 08:44:04 +02:00
Ricardo Wurmus
cda0683295
gnu: r-seurat: Update to 3.1.5. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.5.
[propagated-inputs]: Remove r-metap.
 2020-04-28 08:44:04 +02:00
Roel Janssen
78799a6fdc
gnu: Update minimap2 to 2.17. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.17.
 2020-04-27 21:34:10 +02:00
Roel Janssen
ccf70a80a1
gnu: Add python-deeptools. 
* gnu/packages/bioinformatics.scm (python-deeptools): New variable.
 2020-04-27 13:43:05 +02:00
Roel Janssen
c43edf6f30
gnu: Add python-deeptoolsintervals. 
* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable.
 2020-04-27 13:39:25 +02:00
Efraim Flashner
ee8de73814
gnu: python-scanpy: Update to 1.4.6. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.6.
[arguments]: Add another network based test to skip.
[propagated-inputs]: Add python-tqdm.
 2020-04-26 15:03:50 +03:00
Marius Bakke
7abe35febe
Merge branch 'master' into core-updates 2020-04-19 16:53:01 +02:00
Ricardo Wurmus
974bf81776
gnu: python-pygenometracks: Update to 3.3. 
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.3.
[arguments]: Add phase "relax-requirements"; disable tests.
[propagated-inputs]: Remove python-configparser and python-hicexplorer; add
python-gffutils, python-pysam, and python-tqdm.
 2020-04-17 15:53:03 +02:00
Ricardo Wurmus
d8fce2362b
gnu: Add python-hicmatrix. 
* gnu/packages/bioinformatics.scm (python-hicmatrix): New variable.
 2020-04-17 15:53:03 +02:00
Ricardo Wurmus
c55beaecd8
gnu: python-cooler: Update to 0.8.7. 
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.7.
[propagated-inputs]: Add python-asciitree, python-numpy, python-pyyaml, and
python-simplejson.
[native-inputs]: Remove python-nose, python-numpydoc, and python-sphinx; add
python-pytest.
 2020-04-17 15:53:03 +02:00
Ricardo Wurmus
4a085ffc16
gnu: python-pybigwig: Update to 0.3.17. 
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.17.
 2020-04-17 15:53:03 +02:00
Marius Bakke
bd21acf6c3
Merge branch 'master' into core-updates 2020-04-15 19:26:55 +02:00
Ricardo Wurmus
1971d11db9
gnu: r-delayedarray: Update to 0.12.3. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.3.
[native-inputs]: Add r-knitr.
 2020-04-14 16:41:00 +02:00
Ricardo Wurmus
679609e179
gnu: r-s4vectors: Update to 0.24.4. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.4.
 2020-04-14 16:41:00 +02:00
Ricardo Wurmus
fba62f8e92
gnu: pigx-chipseq: Update to 0.0.42. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.42.
 2020-04-14 14:07:57 +02:00
Marius Bakke
fc58cb5bd2
Merge branch 'master' into core-updates 2020-04-13 20:26:21 +02:00
Vagrant Cascadian
7cc83f43c9
gnu: r-bamsignals: Fix grammar of "allows to efficiently obtain" to 
"efficiently obtains".

* gnu/packages/bioinformatics (r-bamsignals): Fix grammar.
 2020-04-12 14:59:48 -07:00
Vagrant Cascadian
f49369fad2
gnu: r-qtl: Fix grammar "allows to estimate" to "estimates". 
* gnu/packages/bioinformatics (r-qtl): Fix grammar.
 2020-04-12 14:43:50 -07:00
Marius Bakke
bdb90df764
Merge branch 'master' into core-updates 2020-04-11 00:10:23 +02:00
Marius Bakke
bdb56513e7
gnu: minimap2: Fix cond expression for Guile 3 compatibility. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Make the last COND
test the symbol else instead of _.
 2020-04-09 20:04:43 +02:00
Marius Bakke
2778302399
Merge branch 'master' into core-updates 
Conflicts:
	etc/news.scm
	gnu/local.mk
	gnu/packages/check.scm
	gnu/packages/cross-base.scm
	gnu/packages/gimp.scm
	gnu/packages/java.scm
	gnu/packages/mail.scm
	gnu/packages/sdl.scm
	gnu/packages/texinfo.scm
	gnu/packages/tls.scm
	gnu/packages/version-control.scm
 2020-04-08 13:00:50 +02:00
Jakub Kądziołka
7fe746e071
gnu: python-intervaltree: Update to 3.0.2. 
* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2.
[arguments]: Don't skip the tests, work around the problematic
sanity-check instead.
 2020-04-05 20:43:17 +02:00
Marius Bakke
f12f7a0464
gnu: sailfish: Fix build failure. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Prepend to
CPLUS_INCLUDE_PATH instead of overriding it.
 2020-04-03 19:11:05 +02:00
Ricardo Wurmus
0be3cc7f89
gnu: r-biomart: Update to 2.42.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.1.
[native-inputs]: Add r-knitr.
 2020-04-01 11:15:26 +02:00
Ricardo Wurmus
c5c6719f92
gnu: r-genomeinfodb: Update to 1.22.1. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.1.
[native-inputs]: Add r-knitr.
 2020-04-01 11:15:26 +02:00
Marius Bakke
18af687037
Merge branch 'master' into core-updates 
Conflicts:
	gnu/packages/icu4c.scm
	gnu/packages/man.scm
	gnu/packages/python-xyz.scm
	guix/scripts/environment.scm
	guix/scripts/pack.scm
	guix/scripts/package.scm
	guix/scripts/pull.scm
	guix/store.scm
 2020-03-27 00:12:15 +01:00
Roel Janssen
79c395dde3
gnu: Update sambamba to 0.7.1. 
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1;
  Remove unneeded undead input.
 2020-03-26 18:08:27 +01:00
Ricardo Wurmus
c649d31957
gnu: r-tximport: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.2.
[native-inputs]: Add r-knitr.
 2020-03-24 11:06:00 +01:00
Efraim Flashner
10d3fbf051
gnu: edirect: Install more programs. 
* gnu/packages/bioinformatics.scm (edirect)[arguments]: Add
'patch-programs phase to work around not finding binaries in the PATH.
Rewrite 'install phase to install many more scripts. Rewrite
'wrap-program to wrap more scripts with more programs.
[inputs]: Add edirect-go-programs.
[native-search-paths]: New field.
 2020-03-22 09:53:57 +02:00
Efraim Flashner
7d13a94215
gnu: Add edirect-go-programs. 
* gnu/packages/bioinformatics.scm (edirect-go-programs): New variable.
(edirect)[source]: Adjust snippet to not use non-free software.
 2020-03-22 09:53:57 +02:00
Marius Bakke
c4d769d359
Merge branch 'master' into core-updates 2020-03-18 19:41:08 +01:00
Marius Bakke
961d2ee269
Merge branch 'master' into core-updates 2020-03-14 13:13:40 +01:00
Ricardo Wurmus
57f6ac8d90
gnu: pigx-scrnaseq: Update to 1.1.4. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4.
 2020-03-17 20:29:19 +01:00
Ricardo Wurmus
bc6bf142d3
gnu: star: Update to 2.7.3a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.7.3a.
 2020-03-16 13:59:20 +01:00
Marius Bakke
aaadd6e2e1
gnu: salmon: Adjust for C_INCLUDE_PATH changes. 
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Append Eigen headers to
C_INCLUDE_PATH instead of CPATH.
 2020-03-13 00:18:57 +01:00
Efraim Flashner
0c08e4bfa1
gnu: edirect: Update to 13.3.20200128. 
* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128.
[source]: Remove bundled certificate authority tarball.
 2020-03-12 16:50:23 +02:00
Ricardo Wurmus
0b692ef2c6
gnu: r-qtl: Update to 1.46-2. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
 2020-03-12 15:15:02 +01:00
Efraim Flashner
d9a2a255f9
gnu: python-pybedtools: Update to 0.8.1. 
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.1.
[arguments]: Add another test to the 'disable-broken-tests phase.
(python2-pybedtools)[native-inputs]: Add python2-pathlib.
 2020-03-11 16:31:33 +02:00
Efraim Flashner
173053790c
gnu: python-pyfaidx: Update to 0.5.8. 
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.8.
 2020-03-11 15:45:33 +02:00
Efraim Flashner
ea2822d7d6
gnu: Add python2-pyfaidx. 
* gnu/packages/bioinformatics.scm (python2-pyfaidx): New variable.
 2020-03-11 15:43:50 +02:00
Björn Höfling
ec11dcfe69
gnu: java-forester-1.005: Update source URI. 
* gnu/packages/bioinformatics.scm (java-forester-1.005)[source]: Update URI.
[native-inputs]: Wrap long line.
 2020-03-10 23:35:13 +01:00