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Author SHA1 Message Date
Roel Janssen ac370a3397
gnu: r-genomeinfodb: Update to 1.10.2. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.2.
 2017-01-03 12:47:36 +01:00
Ben Woodcroft 25d84d3122
gnu: python-dendropy: Update to 4.2.0. 
* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.2.0.
[source]: Remove patch.
(python2-dendropy)[source]: Use the same source as python-dendropy.
* gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-01-01 16:47:47 +10:00
Ben Woodcroft 322a583fcf
gnu: diamond: Update to 0.8.31. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.31.
 2017-01-01 16:47:47 +10:00
Ben Woodcroft a29929b32c
gnu: multiqc: Update to 0.9. 
Suggested by Raoul Bonnal <ilpuccio.febo@gmail.com>.

* gnu/packages/bioinformatics.scm (multiqc): Update to 0.9.
[origin]: Add patch.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-12-30 17:22:43 +10:00
Ricardo Wurmus 76b64381cb
gnu: r-genomicfeatures: Update to 1.26.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.2.
 2016-12-29 22:24:12 +01:00
Ricardo Wurmus 2f642e5229
gnu: r-biostrings: Update to 2.42.1. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 72c2693b9e
gnu: r-limma: Update to 3.30.7. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.7.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 5796af9981
gnu: r-variantannotation: Update to 1.20.2. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 5d3acc0b36
gnu: r-edger: Update to 3.16.5. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.5.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 81a17b61e7
gnu: r-genomeinfodb: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.1.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 54d9b568fc
gnu: r-iranges: Update to 2.8.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.1.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 86fc9c4a2c
gnu: r-s4vectors: Update to 0.12.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.1.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus c8ad8b6976
gnu: r-biocstyle: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1.
 2016-12-29 22:24:10 +01:00
Ricardo Wurmus 007ee80277
gnu: r-deseq2: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1.
 2016-12-29 22:24:10 +01:00
Ricardo Wurmus d0f0579e6f
gnu: r-annotate: Update to 1.52.1. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1.
[propagated-inputs]: Add r-rcurl.
 2016-12-29 22:24:10 +01:00
Ricardo Wurmus 421f7772b4
gnu: r-qtl: Update to 1.40-8. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.40-8.
 2016-12-29 21:49:09 +01:00
Ricardo Wurmus 2c8d6c0be4
gnu: r-rcas: Update to 1.1.1. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.1.1.
[propagated-inputs]: Add plotrix.
 2016-12-27 14:50:55 +01:00
Ben Woodcroft 9916ef8bb6
gnu: diamond: Update to 0.8.30. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.30.
 2016-12-27 09:18:05 +10:00
Tobias Geerinckx-Rice 33d5b2464d
gnu: cutadapt: Use ‘modify-phases’ syntax. 
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Use
‘modify-phases’.
 2016-12-20 05:36:55 +01:00
Tobias Geerinckx-Rice 1f94bff2d4
gnu: cutadapt: Update to 1.12. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.12.
[inputs]: Add python-xopen.
 2016-12-19 20:33:32 +01:00
Ben Woodcroft 3fffabce2a
gnu: Add attribution line for Raoul Bonnal. 
This is a follow-up commit to c9e9154e99.

* gnu/packages/bioinformatics.scm: Add attribution.
 2016-12-18 10:01:04 +10:00
Raoul Bonnal c9e9154e99
gnu: star: Update to 2.5.2b. 
* gnu/packages/bioinformatics (star): Update to 2.5.2b.
[source]: Delete precompiled binary.

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
 2016-12-17 23:26:35 +10:00
Marius Bakke cdc2bb50b2
gnu: pbtranscript-tofu: Disable tests. 
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Set #:tests? #f.
 2016-12-16 18:15:47 +01:00
Marius Bakke 0d90875974
gnu: multiqc: Fix test dependencies. 
* gnu/packages/bioinformatics.scm (multiqc)[native-inputs]: Add python-nose.
 2016-12-16 13:28:49 +01:00
Marius Bakke 14386fc7d9
gnu: idr: Remove explicit wrapper. This is now done implicitly. 
* gnu/packages/bioinformatics.scm (idr)[arguments]: Remove #:phases.
 2016-12-16 13:16:39 +01:00
Marius Bakke b7a820fc97
gnu: idr: Correct inputs. 
* gnu/packages/bioinformatics.scm (idr)[inputs]: Move everything from here ...
[propagated-inputs]: ... to here. Add python-sympy.
 2016-12-16 13:11:20 +01:00
Marius Bakke 1c10a1d75c
gnu: idr: Disable tests. 
* gnu/packages/bioinformatics.scm (idr)[arguments]: Set #:tests? #f.
 2016-12-16 13:08:57 +01:00
Marius Bakke aaffb9c97b
gnu: deeptools: Fix test dependency. 
* gnu/packages/bioinformatics.scm (deeptools)[native-inputs]: Add python-nose.
 2016-12-16 04:27:35 +01:00
Marius Bakke d281be18bc
gnu: clipper: Fix test dependency. 
* gnu/packages/bioinformatics.scm (clipper)[native-inputs]: Add python2-nose.
 2016-12-16 04:26:32 +01:00
Tobias Geerinckx-Rice 0c6c9c00ab
gnu: Update more dead Google Code home pages. 
* gnu/packages/bioinformatics.scm (cutadapt, mosaik, pepr)[home-page]:
Update to their respective replacements.
 2016-12-14 22:08:51 +01:00
Marius Bakke da5ebd1007
gnu: python-biom-format: Fix tests. 
* gnu/packages/bioinformatics.scm (python-biom-format,
  python2-biom-format)[native-inputs]: Add python-nose.
 2016-12-14 19:18:26 +01:00
Ben Woodcroft 991e143d25
gnu: diamond: Update to 0.8.29. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.29.
 2016-12-13 20:01:56 +10:00
Ben Woodcroft ced1c496aa
gnu: orfm: Update to 0.6.1. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.1.
 2016-12-13 20:00:50 +10:00
Ben Woodcroft 2df3d147ef
gnu: orfm: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.0.
 2016-12-12 20:49:31 +10:00
Ben Woodcroft a225db5293
gnu: vsearch: Update to 2.3.4. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.4.
 2016-12-10 10:45:13 +10:00
Ben Woodcroft 7922ab8fe8
gnu: pardre: Update to 1.1.5-1. 
* gnu/packages/bioinformatics.scm (pardre): update to 1.1.5-1.
[source]: Update source hash.
 2016-12-10 10:45:12 +10:00
Ben Woodcroft 1b7f17ef90
gnu: vsearch: Update to 2.3.3. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.3.
 2016-12-08 22:39:10 +10:00
Ben Woodcroft e990c81d38
gnu: aragorn: Update to 1.2.38. 
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.38.
 2016-12-04 10:51:54 +10:00
Hartmut Goebel 3bf4280659
Merge branch 'master' into python-build-system 2016-11-29 18:47:16 +01:00
Ricardo Wurmus bd3be46e7f
gnu: Add r-gkmsvm. 
* gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
 2016-11-28 22:43:18 +01:00
Ricardo Wurmus 2d9fb1702f
gnu: Add r-seqgl. 
* gnu/packages/bioinformatics.scm (r-seqgl): New variable.
 2016-11-28 22:43:17 +01:00
Ricardo Wurmus c827f20286
gnu: Add r-chipkernels. 
* gnu/packages/bioinformatics.scm (r-chipkernels): New variable.
 2016-11-28 22:43:17 +01:00
Ricardo Wurmus d71605294f
gnu: Add r-wgcna. 
* gnu/packages/bioinformatics.scm (r-wgcna): New variable.
 2016-11-28 22:43:17 +01:00
Ricardo Wurmus e619a5c245
gnu: Add r-r4rna. 
* gnu/packages/bioinformatics.scm (r-r4rna): New variable.
 2016-11-28 22:43:16 +01:00
Ben Woodcroft 9926875572
gnu: Add newick-utils. 
* gnu/packages/bioinformatics.scm (newick-utils): New variable.
 2016-11-28 09:00:41 +10:00
Ben Woodcroft 5e0a0f4226
gnu: roary: Update to 3.7.0. 
* gnu/packages/bioinformatics.scm (roary): Update to 3.7.0.
 2016-11-26 20:15:39 +10:00
Ben Woodcroft 31a9d653ad
gnu: Add proteinortho. 
* gnu/packages/bioinformatics.scm (proteinortho): New variable.
 2016-11-26 20:15:37 +10:00
Leo Famulari de32aa74b4
Merge branch 'master' into python-build-system 2016-11-25 11:20:21 -05:00
Ben Woodcroft 8e5f8c98e2
gnu: diamond: Update to 0.8.27. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27.
 2016-11-22 21:01:21 +10:00
Petter daf72603eb
gnu: Remove redundancy where mkdir-p <dir> is followed by install-file <file> <dir>. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove redundant mkdir-p.
(eigensoft)[arguments]: Likewise.
(snap-aligner)[arguments]: Likewise.
(pardre)[arguments]: Likewise.
(piranha)[arguments]: Likewise.
* gnu/packages/maths.scm (hypre)[arguments]: Likewise.
* gnu/packages/mp3.scm (mpc123)[arguments]: Likewise.
* gnu/packages/music.scm (tuxguitar)[arguments]: Likewise.
* gnu/packages/pdf.scm (impressive)[arguments]: Likewise.
* gnu/packages/qemu.scm (qemu)[arguments]: Likewise.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-11-21 14:39:54 -05:00
Hartmut Goebel de5bc89093
gnu: python2-pbcore: Fix inputs: 
* gnu/packages/bioinformatics.scm (python2-pbcore) [inputs] change to
  [propagated-inputs]. [native-inputs]: Remove python-docutils, which
  comes with sphinx. [former propagated-inputs]: move all (which is only
  pyxb) to [inputs].
 2016-11-15 22:32:01 +01:00
Hartmut Goebel 54c85e12fd
gnu: python2-warpedlmm: Remove phase remove-bin-directory. 
This directory did contain contain wrappers for `nose`, which should not
be there anyway (since nose already was a native-input). The new
python build system no longer creates this directory, while the old one
did. (This difference is due to the bloody details of how packages are
installed.)

* gnu/packages/bioinformatics.scm (python2-warpedlmm)
  [modify-phases] Remove, since remove-bin-directory was the only
  modification here.
 2016-11-15 22:32:00 +01:00
Hartmut Goebel f2516de2fc
gnu: Fix python inputs, part 7: Ensure python-cython is a native-input. 
* gnu/packages/audio.scm (python-pyliblo): [inputs] Move python-cyton to
  [native-inputs].
* gnu/packages/bioinformatics.scm (python2-pybedtools): dito.
* gnu/packages/music.scm (beast, python-pyportmidi): dito.
* gnu/packages/python.scm (python2-fastlmm, python-kivy): dito.
 2016-11-15 22:31:07 +01:00
Hartmut Goebel f22efa0152
gnu: Fix python inputs, part 1: all inputs become propagated-inputs. 
This patch contains the changes where all [inputs] are changed to
[propagated-inputs]

* gnu/packages/python.scm (python-passlib, python-paramiko, python-ccm,
  python-babel, python-keyring python-pandas, python-tzlocal,
  python-parse-type, python-nose2, python-pytest, python-pytest-mock,
  python-pytest-xdist, python-scripttest, python-testtools, python-pytest-cov,
  python-testscenarios, python-pbr-0.11, python-oauthlib, python-jinja2,
  python-sphinx, python-tzlocal, python-bugz, python2-pytest-mock, behave,
  pelican, sqlalchemy-utils, python-pygridtools, python-urwidtrees,
  python-tornado, python2-tornado, python-debian, python-execnet,
  python-pytest-cache, pytest-localserver, python-clint, python-rply,
  python-hy, python-rauth, python-rsa, python-celery, python-vobject, s3cmd,
  python-prompt-toolkit, ptpython, python-requests-oauthlib, python-stem,
  python-binaryornot, python2-binaryornot, python-nltk, python-pymongo,
  python-schematics, python-url, python2-url, python-freezegun,
  python-glances, python-graphql-core, python-graphql-relay, python-graphene,
  python-nautilus, python-s3transfer): All [inputs] become
  [propagated-inputs].
* gnu/packages/bioinformatics.scm (python-biopython): Likewise.
* gnu/packages/django.scm (pytest-django): Likewise.
* gnu/packages/mail.scm (python-mailmanclient): Likewise.
* gnu/packages/password-utils.scm (python-bcrypt): Likewise.
* gnu/packages/propbuf.scm (python-protobuf): Likewise.
* gnu/packages/rdf.scm (python-rdflib): Likewise.

SQACH all become propagated
 2016-11-15 22:31:03 +01:00
Hartmut Goebel b41a05ce49
gnu: Remove work-arounds for bug 20765 (ensure uncompressed eggs). 
Bug 20765 is solved since we build all Python packages using
option "--single-version-externally-managed".

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove
  configure-flags. (pepr): remove phase "disable-egg-generation".
* gnu/packages/pdf.scm (reportlab): Remove configure-flags.
* gnu/packages/python.scm (python-sphinx-rtd-theme, python2-elib.intl,
  python-pkgconfig, python-pytest-pep8, python-pytest-flakes): Remove
  configure-flags. (python-pillow) remove phase
  "disable-egg-generation". (python-libarchive-c) Remove patching
  setup.cfg.
* gnu/packages/statistics.scm (python-patsy): remove phase
  "prevent-generation-of-egg-archive".
* gnu/packages/tls.scm (python-acme): remove phase
  "disable-egg-compression".
* gnu/packages/tor.scm (onionshare): Remove configure-flags.
 2016-11-15 22:31:02 +01:00
Hartmut Goebel 5c31f4aa7c
gnu: Remove python-setuptools and python2-setuptools from inputs (part 4a) 
This patch contains the changes for all modules beside python.scm where
setuptools are used in an inherited package and removing this input also
removes the need for inheriting the package. This is the case if adding
setuptools in the inherited package was the only change.

Change this to not inherit and remove the new needless call to
"strip-python2-variant (if applicable).

* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython,
  python-twobitreader, python2-twobitreader,
  python-plastid, python2-plastid,
  python2-pybigwig,
  python2-screed,
  sra-tools): No longer "inherit" Python 2 packages
  inheriting from a Python 3 package if the sole reason for inheriting was
  adding python-setuptools respective python2-setuptools to [inputs],
  [native-inputs] or [propagated-inputs]. Remove now needless [properties]
  "python2-variant" where applicable.
* gnu/packages/django.scm (python-pytest-django, python2-pytest-django,
  python-django-filter, python2-django-filter): Likewise.
* gnu/packages/gnupg.scm (python2-pygpgme): Likewise.
* gnu/packages/mail.scm (python-mailmanclient, python2-mailmanclient):
  Likewise.
* gnu/packages/mpd.scm (python-msp, python2-mpd2): Likewise.
* gnu/packages/music.scm (python-pylast, python2-pylast): Likewise.
* gnu/packages/openstack.scm (python-requests-mock, python2-requests-mock,
  python2-git-review): Likewise.
* gnu/packages/password-utils.scm (python2-bcrypt): Likewise.
* gnu/packages/protobuf.scm (python-protobuf, python2-protobuf): Likewise.
* gnu/packages/statistics.scm (python-patsy, python2-patsy): Likewise.
* gnu/packages/web.scm (python2-feedparser): Likewise.
 2016-11-15 22:28:59 +01:00
Hartmut Goebel 00e10c6e67
gnu: Remove python-setuptools and python2-setuptools from inputs (part 3) 
This patch contains the changes where setuptools are used in an inherited
package and removing this input keeps the need for inheriting the package.

* gnu/packages/bioinformatics.scm (python2-biom-format): Remove
  python-setuptools respective python2-setuptools from [inputs],
  [native-inputs] and [propagated-inputs] in Python 2 packages inheriting from
  a Python 3 package.
* gnu/packages/python.scm (python2-pytest-mock,
  python2-oauthlib,
  python2-seaborn,
  python2-tornado,
  python2-terminado,
  python2-rauth,
  python2-anyjson,
  python2-amqp,
  python2-kombu,
  python2-billiard,
  python2-celery,
  python2-jellyfish,
  python2-binaryornot,
  python2-natsort,
  python2-graphene): Likewise.
* gnu/packages/statistics.scm (python2-statsmodels): Likewise.
 2016-11-15 22:28:38 +01:00
Hartmut Goebel f3b98f4fec
gnu: Remove python-setuptools and python2-setuptools from inputs (part 2) 
This patch contains the changes where removing setuptools from the inputs
affected some code-lines beside.

* gnu/packages/admin.scm (ansible): Remove all [inputs], [native-inputs] and
  [propagated-inputs] where python-setuptools or python2-setuptools are the
  sole entries. Remove python-setuptools and python2-setuptools listed on a
  line by its own from [inputs], [native-inputs] and [propagated-inputs].

* gnu/packages/backup.scm (duplicity): Likewise.
* gnu/packages/bioinformatics.scm (bamm, python2-pybedtools,
  python2-bx-python, python2-dendropy, python-pysam, python2-pysam, clipper,
  crossmap, cutadapt, deeptools, grit, idr, python2-warpedlmm,
  pbtranscript-tofu, seqmagick): Likewise.
* gnu/packages/docbook.scm (dblatex): Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg, python2-pyxdg): Likewise.
* gnu/packages/lirc.scm (python2-lirc): Likewise.
* gnu/packages/mp3.scm (eyed3): Likewise.
* gnu/packages/nutrition.scm (gourmet): Likewise.
* gnu/packages/openstack.scm (python-hacking, python2-hacking,
  python-os-testr, python2-os-testr,
  python-stevedore, python2-stevedore,
  python-tempest-lib, python2-tempest-lib,
  python-oslo.log, python2-oslo.log,
  python-keystoneclient, python2-keystoneclient): Likewise.
* gnu/packages/password-utils.scm (assword): Likewise.
* gnu/packages/python.scm (python-passlib, python2-passlib,
  python-babel, python2-babel,
  python-parse-type,
  python-pytest, python2-pytest,
  python-scripttest, python2-scripttest,
  python-testtools, python2-testtools,
  python-testscenarios, python2-testscenarios,
  python-subunit, python2-subunit,
  python-pbr-0.11,
  python-pbr, python2-pbr,
  python-testrepository, python2-testrepository,
  behave,
  python-wheel, python2-wheel,
  python-requests, python2-requests,
  python-jsonschema, python2-jsonschema,
  python-pyjwt, python2-pyjwt,
  python-virtualenv, python2-virtualenv,
  python-jinja2, python2-jinja2,
  python-joblib, python2-joblib,
  python-sphinx, python2-sphinx,
  python-feedgenerator, python2-feedgenerator,
  python-scikit-image, python2-scikit-image,
  python-redis, python2-redis,
  python2-fastlmm,
  python-numpydoc, python2-numpydoc,
  python-matplotlib, python2-matplotlib,
  python2-pysnptools,
  python-rpy2, python2-rpy2,
  python-pillow, python2-pillow,
  python-pycparser, python2-pycparser,
  python-cffi, python2-cffi,
  python-cairocffi, python2-cairocffi,
  python-drmaa, python2-drmaa,
  python-pathpy, python2-pathpy,
  python-simplegeneric, python2-simplegeneric,
  python-ipython, python2-ipython,
  python-apsw, python2-apsw,
  python-lxml, python2-lxml,
  python-networkx, python2-networkx,
  python-pyzmq, python2-pyzmq,
  python-mccabe, python2-mccabe,
  python-mccabe-0.2.1,
  python-flake8, python2-flake8,
  python-flake8-2.2.4,
  python-mistune, python2-mistune,
  python-ptyprocess, python2-ptyprocess,
  python-llfuse, python2-llfuse,
  python-webob, python2-webob,
  python-xlrd, python2-xlrd,
  python-tables, python2-tables,
  python-pip, python2-pip,
  python-libarchive-c, python2-libarchive-c,
  python-docopt, python2-docopt,
  python-pyrfc3339, python2-pyrfc3339,
  python-configobj, python2-configobj,
  python-clint, python2-clint,
  python-rply, python2-rply,
  python2-rpython,
  python-widgetsnbextension, python2-widgetsnbextension
  jupyter,
  python-jupyter-console, python2-jupyter-console,
  python-hy, python2-hy,
  python-urllib3, python2-urllib3,
  python-rsa, python2-rsa,
  python-tox, python2-tox,
  python2-hypothesis,
  python-paste, python2-paste,
  python-pastescript, python2-pastescript,
  python2-unicodecsv,
  python-pkgconfig, python2-pkgconfig,
  python2-rope,
  python-sqlparse, python2-sqlparse,
  python-gevent, python2-gevent,
  python-tabulate, python2-tabulate,
  python-arrow, python2-arrow,
  python-cleo, python2-cleo,
  python-fake-factory, python2-fake-factory,
  ptpython): Likewise.
* gnu/packages/rdf.scm (python-rdflib, python2-rdflib): Likewise.
* gnu/packages/terminals.scm (asciinema): Likewise.
* gnu/packages/version-control.scm (git-annex-remote-hubic): Likewise.
* gnu/packages/xdisorg.scm (arandr): Likewise.
 2016-11-15 22:27:31 +01:00
Hartmut Goebel 5d85493284
gnu: Remove python-setuptools and python2-setuptools from inputs (part 1b) 
This patch contains the changes in all modules beside python.scm where
removing setuptools from the inputs could be achieved by removing complete
lines.

* gnu/packages/admin.scm (graphios, thefuck): Remove all [inputs],
  [native-inputs] and [propagated-inputs] where python-setuptools or
  python2-setuptools are the sole entries. Remove python-setuptools and
  python2-setuptools listed on a line by its own from [inputs],
  [native-inputs] and [propagated-inputs].
* gnu/packages/backup.scm (rdiff-backup): Likewise.
* gnu/packages/bioinformatics.scm (htseq, macs, python2-pbcore, rseqc,
  multiqc): Likewise.
* gnu/packages/django.scm (python-django, python2-django,
  python-django-simple-math-captcha, python2-django-simple-math-captcha):
  Likewise.
* gnu/packages/docker.scm (python-docker-py, docker-compose): Likewise.
* gnu/packages/game-development.scm (python-pygame): Likewise.
* gnu/packages/key-mon.scm (key-mon): Likewise.
* gnu/packages/mail.scm (khard): Likewise.
* gnu/packages/music.scm (beets, python2-pyechonest): Likewise.
* gnu/packages/openstack.scm (python-bandit, python2-bandit,
  python-debtcollector, python2-debtcollector,
  python-mox3, python2-mox3,
  python-os-client-config, python2-os-client-config,
  python-oslo.config, python2-oslo.config,
  python-oslo.context, python2-oslo.context,
  python-oslo.i18n, python2-oslo.i18n,
  python-oslo.serialization, python2-oslo.serialization,
  python-oslosphinx, python2-oslosphinx,
  python-oslotest, python2-oslotest,
  python-oslo.utils, python2-oslo.utils,
  python-swiftclient, python2-swiftclient): Likewise.
* gnu/packages/pdf.scm (pdfposter): Likewise.
* gnu/packages/tls.scm (python-acme, python2-acme): Likewise.
 2016-11-15 21:58:44 +01:00
Ricardo Wurmus 84590149e6
gnu: hisat: Fix typo. 
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Fix directory
name in install phase.
 2016-11-15 20:21:08 +01:00
Ricardo Wurmus 7c45670b32
gnu: r-org-mm-eg-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.4.0.
 2016-11-11 09:08:08 +01:00
Ricardo Wurmus 0cfac6f270
gnu: r-org-dm-eg-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.4.0.
 2016-11-11 09:08:08 +01:00
Ricardo Wurmus f04a3eff98
gnu: r-org-ce-eg-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.4.0.
 2016-11-11 09:08:08 +01:00
Ricardo Wurmus 83f9a6fb60
gnu: r-org-hs-eg-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.4.0.
 2016-11-11 09:08:07 +01:00
Ben Woodcroft 3cf7c31720
gnu: diamond: Update to 0.8.26. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.26.
 2016-11-07 21:31:09 +10:00
Ricardo Wurmus ed8fbe5e62
gnu: r-rcas: Update to 1.0.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.0.0.
 2016-11-03 19:01:46 +01:00
Ricardo Wurmus 16a8bd3194
gnu: r-rtracklayer: Update to 1.34.1. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.1.
 2016-11-03 19:01:46 +01:00
Ricardo Wurmus c15ae9b008
gnu: r-biocparallel: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.1.
 2016-11-03 19:01:46 +01:00
Ricardo Wurmus 5b3b2d2f02
gnu: r-limma: Update to 3.30.2. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.2.
 2016-11-03 19:01:46 +01:00
Ricardo Wurmus ed3054231d
gnu: r-edger: Update to 3.16.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.1.
 2016-11-03 19:01:45 +01:00
Leo Famulari 044ac8d294
gnu: python-twobitreader: Update to 3.1.4. 
* gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader):
Update to 3.1.4.
 2016-10-28 13:59:11 -04:00
Leo Famulari 900fb8d005
gnu: python-twobitreader: Disable the test suite. 
The tests were silently skipped with Python 3.4. With Python 3.5, this caused
the build of python-twobitreader to fail.

* gnu/packages/bioinformatics.scm (python-twobitreader,
python2-twobitreader)[arguments]: Disable the tests.
 2016-10-28 13:59:11 -04:00
Roel Janssen 7500e42b3e
gnu: Add r-mutationalpatterns. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
 2016-10-27 20:07:05 +02:00
Ricardo Wurmus a46cc723ff
gnu: r-seqinr: Update to 3.3-3. 
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-3.
 2016-10-26 16:23:26 +02:00
Ricardo Wurmus c70271ec48
gnu: bioperl-minimal: Update to 1.7.0. 
* gnu/packages/bioinformatics.scm (bioperl-minimal): Update to 1.7.0.
 2016-10-26 16:23:24 +02:00
Ricardo Wurmus 59198f8fff
gnu: r-genomationdata: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.6.0.
 2016-10-26 09:28:23 +02:00
Ricardo Wurmus e357bec836
gnu: r-bamsignals: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.6.0.
 2016-10-26 09:28:23 +02:00
Ricardo Wurmus 53ca52f013
gnu: r-rhtslib: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.6.0.
[native-inputs]: Add autoconf.
 2016-10-26 09:28:23 +02:00
Ricardo Wurmus da22da862b
gnu: r-zlibbioc: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.20.0.
 2016-10-26 09:28:22 +02:00
Ricardo Wurmus 809251e164
gnu: r-motifrg: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.18.0.
 2016-10-26 09:28:22 +02:00
Ricardo Wurmus 21d6c7a3e1
gnu: r-seqlogo: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.40.0.
 2016-10-26 09:28:22 +02:00
Ricardo Wurmus 51c3c4900f
gnu: r-genomation: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.6.0.
[propagated-inputs]: Add r-rcpp, r-htslib, r-runit, r-s4vectors.
[inputs]: Add zlib.
 2016-10-26 09:28:21 +02:00
Ricardo Wurmus e92dd6f5e0
gnu: r-seqpattern: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.6.0.
[propagated-inputs]: Add r-kernsmooth.
 2016-10-26 09:28:21 +02:00
Ricardo Wurmus acf6f7e0c3
gnu: r-impute: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.48.0.
 2016-10-26 09:28:21 +02:00
Ricardo Wurmus 3d74c04451
gnu: r-bsgenome: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.42.0.
 2016-10-26 09:28:20 +02:00
Ricardo Wurmus 30ec4de738
gnu: r-topgo: Update to 2.26.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0.
[propagated-inputs]: Add r-dbi.
 2016-10-26 09:28:20 +02:00
Ricardo Wurmus 3587b464fc
gnu: r-graph: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0.
 2016-10-26 09:28:19 +02:00
Ricardo Wurmus d1b1587cad
gnu: r-go-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.4.0.
 2016-10-26 09:28:19 +02:00
Ricardo Wurmus b17aac083e
gnu: r-genomicfeatures: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.0.
 2016-10-26 09:28:18 +02:00
Ricardo Wurmus 6a45fd9aea
gnu: r-rtracklayer: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0.
 2016-10-26 09:28:18 +02:00
Ricardo Wurmus 4ab32f0cd6
gnu: r-genomicalignments: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to
1.10.0.
 2016-10-26 09:28:18 +02:00
Ricardo Wurmus 08da08d296
gnu: r-summarizedexperiment: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to
1.4.0.
 2016-10-26 09:28:17 +02:00
Ricardo Wurmus c0ccef41ae
gnu: r-rsamtools: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1.
 2016-10-26 09:28:17 +02:00
Ricardo Wurmus 47d39b6e7a
gnu: r-biostrings: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0.
 2016-10-26 09:28:17 +02:00
Ricardo Wurmus 89559a124e
gnu: r-biocparallel: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus 9405333186
gnu: r-biomart: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus e45dc05781
gnu: r-annotationdbi: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus 464870caf7
gnu: r-biobase: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0.
 2016-10-26 09:28:15 +02:00
Ricardo Wurmus 92a740afac
gnu: r-genomicranges: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.1.
[propagated-inputs]: Add r-iranges, r-s4vectors.
 2016-10-26 09:28:15 +02:00
Ricardo Wurmus 1d048589ca
gnu: r-xvector: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus 753bc32b8e
gnu: r-limma: Update to 3.30.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus 37d96f1dde
gnu: r-variantannotation: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to
1.20.0.
[propagated-inputs]: Add r-biobase, r-biostrings, r-iranges,
r-rtracklayer, r-s4vectors, r-xvector.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus 5e48005fa9
gnu: r-edger: Update to 3.16.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0.
[propagated-inputs]: Add r-locfit.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus dece310a25
gnu: r-genomeinfodb: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0.
 2016-10-26 09:28:13 +02:00
Ricardo Wurmus 7f354dafb1
gnu: r-iranges: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0.
 2016-10-26 09:28:13 +02:00
Ricardo Wurmus b120c5f3a2
gnu: r-s4vectors: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.0.
 2016-10-26 09:28:13 +02:00
Ricardo Wurmus 22c5d736af
gnu: r-dnacopy: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.48.0.
 2016-10-26 09:28:12 +02:00
Ricardo Wurmus 5c7b04e0c3
gnu: r-biocinstaller: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.24.0.
 2016-10-26 09:28:12 +02:00
Ricardo Wurmus f0b297e17b
gnu: r-biocgenerics: Update to 0.20.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.20.0.
 2016-10-26 09:28:11 +02:00
Ricardo Wurmus c9b5046a18
gnu: r-grohmm: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.8.0.
 2016-10-26 09:28:11 +02:00
Ricardo Wurmus 1265d3877b
gnu: r-systempiper: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.8.1.
 2016-10-26 09:28:11 +02:00
Ricardo Wurmus b87b41a74d
gnu: r-shortread: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.0.
 2016-10-26 09:28:10 +02:00
Ricardo Wurmus ae6899b683
gnu: r-gostats: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.40.0.
 2016-10-26 09:28:10 +02:00
Ricardo Wurmus 816599c1e7
gnu: r-category: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.40.0.
 2016-10-26 09:28:10 +02:00
Ricardo Wurmus 558d02c361
gnu: r-gseabase: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.36.0.
 2016-10-26 09:28:09 +02:00
Ricardo Wurmus 700c780dcf
gnu: r-rbgl: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.50.0.
 2016-10-26 09:28:09 +02:00
Ricardo Wurmus 55cd914c3d
gnu: r-annotationforge: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.0.
[propagated-inputs]: Add r-rcurl.
 2016-10-26 09:28:09 +02:00
Ricardo Wurmus e1db8dd813
gnu: r-deseq2: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.0.
 2016-10-26 09:28:08 +02:00
Ricardo Wurmus 1e66e71921
gnu: r-genefilter: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.56.0.
 2016-10-26 09:28:08 +02:00
Ricardo Wurmus 6faa2a48f0
gnu: r-geneplotter: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.52.0.
 2016-10-26 09:28:08 +02:00
Ricardo Wurmus 9beba74f66
gnu: r-annotate: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.0.
 2016-10-26 09:28:07 +02:00
Roel Janssen 4644644ace
gnu: Add r-bioccheck. 
* gnu/packages/bioinformatics.scm (r-bioccheck): New variable.
 2016-10-20 09:53:02 +02:00
Roel Janssen 99df12cd19
gnu: Add r-biocstyle. 
* gnu/packages/bioinformatics.scm (r-biocstyle): New variable.
 2016-10-19 15:22:06 +02:00
Roel Janssen 207ce8fbe5
gnu: Add r-biocviews. 
* gnu/packages/bioinformatics.scm (r-biocviews): New variable.
 2016-10-19 15:09:55 +02:00
Roel Janssen c79ad57a8d
gnu: Add r-optparse. 
* gnu/packages/bioinformatics.scm (r-optparse): New variable.
 2016-10-19 10:48:56 +02:00
Roel Janssen 2acaaee550
gnu: Add r-getopt. 
* gnu/packages/bioinformatics.scm (r-getopt): New variable.
 2016-10-19 09:55:45 +02:00
Ricardo Wurmus 5093729704
gnu: Add rcas-web. 
* gnu/packages/bioinformatics.scm (rcas-web): New variable.
 2016-10-17 18:09:20 +02:00
Ricardo Wurmus 89984be46e
gnu: Add r-rcas. 
* gnu/packages/bioinformatics.scm (r-rcas): New variable.
 2016-10-17 18:09:16 +02:00
Ben Woodcroft 3dd50d974b
gnu: vsearch: Update to 2.3.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.0.
 2016-10-11 22:29:48 +10:00
Ben Woodcroft 99c9056141
gnu: diamond: Update to 0.8.23. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.23.
 2016-10-11 19:51:49 +10:00
Ben Woodcroft 9602e3cce9
gnu: python2-dendropy: Fix tests. 
* gnu/packages/bioinformatics.scm (python2-dendropy)[source]: Use unpatched
source.
[arguments]: Use nose to run tests.
[native-inputs]: Add python2-nose.
 2016-10-08 21:38:17 +10:00
Ricardo Wurmus fc47c7d635
gnu: Add r-bsgenome-celegans-ucsc-ce10. 
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10): New
variable.
 2016-10-06 10:33:43 +02:00
Ben Woodcroft 2c3eb4b85b
gnu: metabat: Update to 0.32.4-1.cbdca756. 
* gnu/packages/bioinformatics.scm (metabat): Update to 0.32.4-1.cbdca756.
* gnu/packages/patches/metabat-remove-compilation-date.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-10-04 22:02:52 +10:00
Ben Woodcroft 4bdc3df92d
gnu: vsearch: Update to 2.1.2. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.2.
 2016-10-02 22:25:39 +10:00
Ricardo Wurmus 2320e76b82
gnu: sra-tools: Fix build on i686. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Pass
"VDB_LIBDIR" in make-flags; dynamically link libmagic.
 2016-09-28 22:30:41 +02:00
Ben J Woodcroft 99caa6f75f
gnu: python-plastid: Update to 1.4.6. 
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): Update to
1.4.6.
[propagated-inputs]: Add python-termcolor.
 2016-09-27 20:07:12 +10:00
Marius Bakke f536dce522
gnu: python-pysam: Enable tests. 
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from
PyPi to source archive due to missing test data.
[arguments]: Add check phase after install.
[native-inputs]: Add python-nose, samtools and bcftools.
 2016-09-27 20:06:00 +10:00
Marius Bakke dff26b2363
gnu: python-pysam: Delete bundled htslib. 
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet
to delete htslib.
[arguments]: Add htslib flags in 'set-flags phase.
[propagated-inputs]: New field. Add htslib.
 2016-09-27 20:06:00 +10:00
Marius Bakke 397d463a12
gnu: python-pysam: Use 'modify-phases'. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Use
'modify-phases'.
 2016-09-27 20:06:00 +10:00
Marius Bakke bdc7be59eb
gnu: Add bcftools. 
* gnu/packages/bioinformatics.scm (bcftools): New variable.
 2016-09-27 20:06:00 +10:00
Marius Bakke e301bfc886
gnu: python2-pbcore: Update to 1.2.10. 
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.10.
[propagated-inputs]: New field. Add python2-pyxb.
 2016-09-27 20:06:00 +10:00
Marius Bakke fd49eb213f
gnu: python-pysam: Update to 0.9.1.4. 
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): Update
to 0.9.1.4.
 2016-09-27 20:05:57 +10:00
Ricardo Wurmus 675d7ae26f
gnu: ncbi-vdb: Only build on i686 and x86_64. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[supported-systems]: Only
build on i686 and x86_64.
[arguments]: Add mandatory "-msse2" flag to CFLAGS.
 2016-09-26 14:30:59 +02:00
Ben Woodcroft af8de20386
gnu: vsearch: Update to 2.1.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.1.
 2016-09-26 20:35:32 +10:00
Ricardo Wurmus f3cfe4515a
gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene. 
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene):
  New variable.
 2016-09-26 07:47:55 +02:00
Ricardo Wurmus 684f29bd2e
gnu: Add r-grohmm. 
* gnu/packages/bioinformatics.scm (r-grohmm): New variable.
 2016-09-26 07:47:55 +02:00
Ricardo Wurmus 7f903d7300
gnu: Add r-systempiper. 
* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
 2016-09-26 07:47:55 +02:00
Ricardo Wurmus cb99d457f0
gnu: Add r-shortread. 
* gnu/packages/bioinformatics.scm (r-shortread): New variable.
 2016-09-26 07:47:54 +02:00
Ricardo Wurmus 89f40c5e4e
gnu: Add r-gostats. 
* gnu/packages/bioinformatics.scm (r-gostats): New variable.
 2016-09-26 07:47:54 +02:00
Ricardo Wurmus 1a1931f7e0
gnu: Add r-category. 
* gnu/packages/bioinformatics.scm (r-category): New variable.
 2016-09-26 07:47:54 +02:00
Ricardo Wurmus ad740ff818
gnu: Add r-gseabase. 
* gnu/packages/bioinformatics.scm (r-gseabase): New variable.
 2016-09-26 07:47:53 +02:00
Ricardo Wurmus cd9e7dc7ff
gnu: Add r-rbgl. 
* gnu/packages/bioinformatics.scm (r-rbgl): New variable.
 2016-09-26 03:25:23 +02:00
Ricardo Wurmus e816377374
gnu: Add r-annotationforge. 
* gnu/packages/bioinformatics.scm (r-annotationforge): New variable.
 2016-09-26 03:25:17 +02:00
Ricardo Wurmus ad34f0ac96
gnu: Add r-deseq2. 
* gnu/packages/bioinformatics.scm (r-deseq2): New variable.
 2016-09-26 03:21:27 +02:00
Ricardo Wurmus 2301fd3e4d
gnu: Add r-genefilter. 
* gnu/packages/bioinformatics.scm (r-genefilter): New variable.
 2016-09-26 03:21:19 +02:00
Ricardo Wurmus 07a664cde0
gnu: Add r-geneplotter. 
* gnu/packages/bioinformatics.scm (r-geneplotter): New variable.
 2016-09-26 03:21:07 +02:00
Ricardo Wurmus 8c6de58849
gnu: Add r-annotate. 
* gnu/packages/bioinformatics.scm (r-annotate): New variable.
 2016-09-26 03:20:59 +02:00
Ricardo Wurmus 646a84338d
gnu: sra-tools: Update to 2.7.0. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.7.0.
 2016-09-23 11:46:53 +02:00
Ricardo Wurmus 40974c933e
gnu: ncbi-vdb: Update to 2.7.0. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.7.0.
 2016-09-23 11:46:26 +02:00
Ricardo Wurmus 48b419ebd6
gnu: ngs-sdk: Update to 1.2.5. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.5.
 2016-09-23 11:45:24 +02:00
Efraim Flashner 0dbb7ac2df
gnu: plink: Set endian-ness on more architectures. 
* gnu/packages/patches/plink-endian-detection.patch: New file.
* gnu/packages/bioinformatics.scm (plink)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Register it.
 2016-09-22 22:42:37 +03:00
Efraim Flashner 62d00095c2
gnu: prank: Allow building on 32-bit machines. 
* gnu/packages/bioinformatics.scm (prank)[arguments]: Add a phase
removing the '-m64' compiler flag.
 2016-09-22 19:21:16 +03:00
Ben Woodcroft 951da521a9
gnu: diamond: Update to 0.8.22. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.22.
 2016-09-22 16:36:00 +10:00
Efraim Flashner 6e8faf7794
gnu: jellyfish: Limit to x86_64. 
* gnu/packages/bioinformatics.scm (jellyfish)[supported-systems}: New
field, limit support to x86_64.
 2016-09-21 22:36:52 +03:00
Ben Woodcroft 79558df220
gnu: vsearch: Update to 2.1.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.0.
 2016-09-21 18:44:22 +10:00
Roel Janssen eb24341ffb
gnu: Add r-biocinstaller. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): New variable.
 2016-09-19 11:56:44 +02:00
Ben Woodcroft de96ea286d
gnu: python-biom-format: Move inputs to propagated-inputs. 
* gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format)
[inputs]: Move all from here ...
[propagated-inputs]: ... to here.
 2016-09-19 15:44:20 +10:00
Ben Woodcroft 7bba95b769
gnu: seqmagick: Use BioPython 1.66. 
* gnu/packages/bioinformatics.scm (seqmagick)[inputs]: Use
python2-biopython-1.66 instead of python2-biopython.
 2016-09-19 15:44:20 +10:00
Ben Woodcroft 4b1a152826
gnu: Add python2-biopython-1.66. 
* gnu/packages/bioinformatics.scm (python2-biopython-1.66): New variable.
 2016-09-19 15:44:20 +10:00
Ben Woodcroft 8c8da1389e
gnu: python-biopython: Use 'python2-variant'. 
* gnu/packages/bioinformatics.scm (python-biopython)[properties]: New field.
[native-inputs]: Remove field.
(python-biopython): Use 'strip-python-variant'.
 2016-09-19 15:44:20 +10:00
Ben Woodcroft 4ce6030588
gnu: python-biopython: Update to 1.68. 
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.68.
[arguments]: New field.
 2016-09-19 15:44:18 +10:00
Ben J Woodcroft 66daf78c0a
gnu: Add seqtk. 
* gnu/packages/bioinformatics.scm (seqtk): New variable.
 2016-09-13 20:27:29 +10:00
Leo Famulari 2642231b39
gnu: bowtie: Update to 2.2.9. 
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.9.
 2016-09-12 14:19:37 -04:00
Ricardo Wurmus d108c21228
gnu: r-org-mm-eg-db: Update to 3.3.0. 
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.3.0.
 2016-09-12 17:44:49 +02:00
Ricardo Wurmus 6ab7ca24f2
gnu: r-org-dm-eg-db: Update to 3.3.0. 
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.3.0.
 2016-09-12 17:44:48 +02:00
Ricardo Wurmus 019be09060
gnu: r-org-ce-eg-db: Update to 3.3.0. 
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.3.0.
 2016-09-12 17:44:48 +02:00
Ricardo Wurmus 5cc7cff6ef
gnu: r-org-hs-eg-db: Update to 3.3.0. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.3.0.
 2016-09-12 17:44:48 +02:00
Ricardo Wurmus 401528b2b5
gnu: r-go-db: Update to 3.3.0. 
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.3.0.
 2016-09-12 17:44:48 +02:00
Ricardo Wurmus 44f711dbe6
gnu: r-biocparallel: Update to 1.6.6. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.6.
 2016-09-12 17:44:42 +02:00
Ricardo Wurmus 10e479a7c0
gnu: r-genomicranges: Update to 1.24.3. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.3.
 2016-09-12 17:44:42 +02:00
Ricardo Wurmus 01ebbb1b76
gnu: r-limma: Update to 3.28.21. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.21.
 2016-09-12 17:44:42 +02:00
Ricardo Wurmus bbf53cb527
gnu: r-variantannotation: Update to 1.18.7. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.7.
 2016-09-12 17:44:42 +02:00
Ricardo Wurmus 4fa7091d54
gnu: r-genomeinfodb: Update to 1.8.7. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.7.
 2016-09-12 17:44:41 +02:00
Ricardo Wurmus 3b851cd4ac
gnu: r-seqinr: Update to 3.3-1. 
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-1.
[propagated-inputs]: Add "r-segmented".
 2016-09-12 17:44:41 +02:00
Ricardo Wurmus 2b1cc79d98
gnu: r-s4vectors: Update to 0.10.3. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.3.
 2016-09-12 17:44:41 +02:00
Ricardo Wurmus 0b54b4c986
gnu: r-acsnminer: Update to 0.16.8.25. 
* gnu/packages/bioinformatics.scm (r-acsnminer): Update to 0.16.8.25.
 2016-09-12 17:44:41 +02:00
Ricardo Wurmus 2c575bb9a2
gnu: r-vegan: Update to 2.4-1. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-1.
 2016-09-12 17:44:40 +02:00
Marius Bakke 84be3b9920
gnu: Add mash. 
* gnu/packages/bioinformatics.scm (mash): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-09-10 17:41:38 -04:00
Ben Woodcroft 4b6da268ff
gnu: bamm: Update to 1.7.3. 
* gnu/packages/bioinformatics.scm (bamm): Update to 1.7.3.
 2016-09-10 09:47:42 +10:00
Efraim Flashner 48409ef269
gnu: infernal: Limit to i686 and x86_64 systems. 
* gnu/packages/bioinformatics.scm (infernal)[supported-systems]: The
package requires VMX or SSE capability for parallel instructions, so
limit it to those supported systems.
 2016-09-04 12:43:10 +03:00
Ricardo Wurmus 35aa90a1fd
gnu: Add Infernal. 
* gnu/packages/bioinformatics.scm (infernal): New variable.
 2016-09-02 16:46:37 +02:00
Ricardo Wurmus c180533bb5
gnu: subread: Update to 1.5.1. 
* gnu/packages/bioinformatics.scm (subread): Update to 1.5.1.
 2016-08-31 15:23:03 +02:00
Ben Woodcroft 7d57ebaa7c
gnu: aragorn: Update to 1.2.37. 
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.37.
 2016-08-31 15:52:49 +10:00
Ben Woodcroft caa9bc7dc5
gnu: diamond: Update to 0.8.20. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.20.
 2016-08-30 10:46:30 +10:00
Ricardo Wurmus fe02c4c98a
gnu: Add r-bamsignals. 
* gnu/packages/bioinformatics.scm (r-bamsignals): New variable.
 2016-08-22 16:52:40 +02:00
Ricardo Wurmus 52765a63ca
gnu: Add r-rhtslib. 
* gnu/packages/bioinformatics.scm (r-rhtslib): New variable.
 2016-08-22 16:52:22 +02:00
Ricardo Wurmus 433530a5fc
gnu: clipper: Update to 1.1. 
* gnu/packages/bioinformatics.scm (clipper): Update to 1.1.
[source]: Delete pre-built libraries.
[inputs]: Add python2-pandas.
 2016-08-17 19:35:05 +02:00
Marius Bakke 318c0aee1e
gnu: Add minced. 
* gnu/packages/bioinformatics.scm (minced): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2016-08-17 20:56:21 +10:00
Ben Woodcroft 71461f88ee
gnu: mafft: Update to 7.305. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.305.
[inputs]: Add ruby.
 2016-08-16 19:49:15 +10:00
Ben Woodcroft 0ed8f0cd4c
gnu: mafft: Update to 7.304. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.304.
 2016-08-15 20:59:41 +10:00
Ben Woodcroft 101e8f7171
gnu: mafft: Wrap programs. 
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Add 'wrap-programs'
phase.
[propagated-inputs]: Move coreutils from here ...
[inputs]: ... to here.
 2016-08-15 20:51:00 +10:00
Ben Woodcroft 93b8316e08
gnu: mafft: Update to 7.300. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.300.
 2016-08-15 20:51:00 +10:00
Ben Woodcroft a12ba6e878
gnu: Add bamm. 
* gnu/packages/bioinformatics.scm (bamm): New variable.
 2016-08-14 14:55:23 +10:00
Efraim Flashner 3e6fdd5f8a
gnu: snap-aligner: Limit to x86_64. 
* gnu/packages/bioinformatics.scm (snap-aligner)[supported-systems]: Add
note explaining why we build for x86_64 only.
 2016-08-11 22:44:07 +03:00
Ben Woodcroft 7024aeaaaa
gnu: diamond: Update to 0.8.18. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.18.
 2016-08-11 20:39:54 +10:00
Ben Woodcroft ceb62d5436
gnu: Add roary. 
* gnu/packages/bioinformatics.scm (roary): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 608dd93267
gnu: Add raxml. 
* gnu/packages/bioinformatics.scm (raxml): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 024130d258
gnu: Add prank. 
* gnu/packages/bioinformatics.scm (prank): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft b16728b068
gnu: Add exonerate. 
* gnu/packages/bioinformatics.scm (exonerate): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft db7a344427
gnu: Add bppsuite. 
* gnu/packages/bioinformatics.scm (bppsuite): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 159a701678
gnu: Add bpp-popgen. 
* gnu/packages/bioinformatics.scm (bpp-popgen): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 8b5f4d5700
gnu: Add bpp-phyl. 
* gnu/packages/bioinformatics.scm (bpp-phyl): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 70f1bc051a
gnu: Add bpp-seq. 
* gnu/packages/bioinformatics.scm (bpp-seq): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 985d841144
gnu: Add bpp-core. 
* gnu/packages/bioinformatics.scm (bpp-core): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 9e12eba866
gnu: Add python-biom-format. 
* gnu/packages/bioinformatics.scm (python-biom-format,
python2-biom-format): New variables.
 2016-08-06 09:44:28 +10:00
Ricardo Wurmus 97b9da6897
gnu: Add discrover. 
* gnu/packages/bioinformatics.scm (discrover): New variable.
 2016-08-03 17:20:26 +02:00
Ben Woodcroft afde1a264b
gnu: fxtract: Restrict to x86_64-linux. 
* gnu/packages/bioinformatics.scm (fxtract)[supported-systems]: Restrict to
  x86_64-linux.
 2016-08-03 21:22:02 +10:00
Ricardo Wurmus dda3627141
gnu: r-variantannotation: Update to 1.18.6. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.6.
 2016-08-02 14:47:46 +02:00
Ricardo Wurmus 005ca42396
gnu: r-genomationdata: Update to 1.4.2. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.4.2.
 2016-08-02 14:47:46 +02:00
Ben Woodcroft c4382cd18f
gnu: diamond: Update to 0.8.17. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.17.
 2016-07-30 23:02:57 +10:00
Ben Woodcroft 6547708f71
gnu: r-genomicfeatures: Update to 1.24.5. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
 2016-07-28 21:54:44 +10:00
Ben Woodcroft 2c9f6251fc
gnu: r-bsgenome: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
 2016-07-28 21:45:17 +10:00
Ben Woodcroft b0f0778a7c
gnu: r-iranges: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
 2016-07-28 21:45:17 +10:00
Ben Woodcroft f403941f81
gnu: r-limma: Update to 3.28.17. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft 2b2ff0bd91
gnu: r-xvector: Update to 0.12.1. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft a463055862
gnu: r-genomicranges: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft bab15ccec4
gnu: r-annotationdbi: Update to 1.34.4. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft a22999f245
gnu: r-biocparallel: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft d104fc607d
gnu: r-biostrings: Update to 2.40.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft 1864e051c9
gnu: r-summarizedexperiment: Update to 1.2.3. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft 29b0cc8ad5
gnu: r-genomicalignments: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft 5131e21064
gnu: r-rtracklayer: Update to 1.32.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft 2a3e325f5e
gnu: r-genomeinfodb: Update to 1.8.3. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft f2e791750b
gnu: r-s4vectors: Update to 0.10.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
 2016-07-28 20:13:42 +10:00
Ben Woodcroft 12c8f210ee
gnu: diamond: Update to 0.8.16. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16.
 2016-07-27 23:17:57 +10:00
Ben Woodcroft e03a515304
gnu: fasttree: Update to 2.1.9. 
* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.9.
 2016-07-23 15:15:12 +10:00
Leo Famulari de67e92288
gnu: Update URLs for sourceforge.net. 
* gnu/packages/admin.scm: Update URLs pointing to sourceforge.net.
* gnu/packages/audacity.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/boost.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/code.scm: Likewise.
* gnu/packages/compression.scm: Likewise.
* gnu/packages/cups.scm: Likewise.
* gnu/packages/djvu.scm: Likewise.
* gnu/packages/docbook.scm: Likewise.
* gnu/packages/documentation.scm: Likewise.
* gnu/packages/flashing-tools.scm: Likewise.
* gnu/packages/fonts.scm: Likewise.
* gnu/packages/fontutils.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/ghostscript.scm: Likewise.
* gnu/packages/gl.scm: Likewise.
* gnu/packages/gnucash.scm: Likewise.
* gnu/packages/graphviz.scm: Likewise.
* gnu/packages/image.scm: Likewise.
* gnu/packages/libreoffice.scm: Likewise.
* gnu/packages/libusb.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/lirc.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mcrypt.scm: Likewise.
* gnu/packages/mp3.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/networking.scm: Likewise.
* gnu/packages/onc-rpc.scm: Likewise.
* gnu/packages/password-utils.scm: Likewise.
* gnu/packages/pdf.scm: Likewise.
* gnu/packages/perl.scm: Likewise.
* gnu/packages/photo.scm: Likewise.
* gnu/packages/popt.scm: Likewise.
* gnu/packages/python.scm: Likewise.
* gnu/packages/rdesktop.scm: Likewise.
* gnu/packages/screen.scm: Likewise.
* gnu/packages/swig.scm: Likewise.
* gnu/packages/tcl.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/w3m.scm: Likewise.
* gnu/packages/web.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xml.scm: Likewise.
 2016-07-21 18:09:40 -04:00
Ben Woodcroft 7593e50b26
gnu: diamond: Update to 0.8.15. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.15.
 2016-07-18 00:06:21 +10:00
Ricardo Wurmus 2c0d8e0d09
gnu: eigensoft: Do not refer to "lapacke" output. 
* gnu/packages/bioinformatics.scm (eigensoft)[inputs]: Remove reference
  to non-existing "lapacke" output.
 2016-07-17 12:04:04 +02:00
Ricardo Wurmus 6619f9c769
gnu: Add eigensoft. 
* gnu/packages/bioinformatics.scm (eigensoft): New variable.
 2016-07-14 08:58:35 +02:00
Ricardo Wurmus 17dc32a400
gnu: Add Ribotaper. 
* gnu/packages/bioinformatics.scm (ribotaper): New variable.
 2016-07-12 12:19:39 +02:00
Ricardo Wurmus 9a8f309cf1
gnu: Add bedtools-2.18. 
* gnu/packages/bioinformatics.scm (bedtools-2.18): New variable.
 2016-07-12 12:19:15 +02:00
Ben Woodcroft 7f575d3e56
gnu: diamond: Update to 0.8.12. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.12.
 2016-07-10 22:32:57 +10:00
Ben Woodcroft ec2a67de88
gnu: Add python-dendropy. 
* gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy): New
variables.
* gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-07-09 08:00:34 +10:00
Ben Woodcroft c11f79a49e
gnu: star: Restrict supported systems to 64-bit systems. 
* gnu/packages/bioinformatics.scm (star)[supported-systems]: Restrict to
x86_64-linux and mips64el-linux.
 2016-07-08 22:10:05 +10:00
Ben Woodcroft d285657eae
gnu: bedtools: Update to 2.26.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.26.0.
 2016-07-07 23:27:19 +10:00
Ben Woodcroft 7c7643a7f0
gnu: diamond: Update to 0.8.11. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.11.
 2016-07-07 18:21:10 +08:00
Ricardo Wurmus 274da826f9
gnu: Add r-seqinr. 
* gnu/packages/bioinformatics.scm (r-seqinr): New variable.
 2016-07-07 10:46:17 +02:00
Efraim Flashner 8157af2e09
gnu: khmer: Limit to x86_64 systems only. 
* gnu/packages/bioinformatics.scm (khmer)[supported-systems]: New field.
 2016-07-07 06:33:28 +03:00
Ricardo Wurmus 5fb5dffbd4
gnu: Add multiqc. 
* gnu/packages/bioinformatics.scm (multiqc): New variable.
 2016-07-05 16:32:37 +02:00
Ricardo Wurmus 1f1b20b8be
gnu: Add bits. 
* gnu/packages/bioinformatics.scm (bits): New variable.
 2016-07-05 15:43:36 +02:00
Ricardo Wurmus 66e40e0065
gnu: Add EMBOSS. 
* gnu/packages/bioinformatics.scm (emboss): New variable.
 2016-07-05 12:32:12 +02:00
Roel Janssen 744004a31f
gnu: Add r-edger. 
* gnu/packages/bioinformatics.scm (r-edger): New variable.
 2016-07-04 14:49:07 +02:00
Roel Janssen 7d4224d794
gnu: Add r-limma. 
* gnu/packages/bioinformatics.scm (r-limma):  New variable.
 2016-07-04 14:39:16 +02:00
Ben Woodcroft 71830f0e49
gnu: vsearch: Update to 2.0.1. 
*  gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.1.
 2016-07-01 09:01:28 +10:00
Ben Woodcroft 8dec2229a2
gnu: blast+: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (blast+): Update to 2.4.0.
 2016-06-29 22:42:47 +10:00
Ben Woodcroft 3bce0f14b2
gnu: star: Update to 2.5.2a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.5.2a.
 2016-06-29 10:14:22 +10:00
Ben Woodcroft 6c737963f6
gnu: htslib: Update to 1.3.1. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.3.1.
 2016-06-29 10:14:22 +10:00
Ricardo Wurmus ec9466388e
gnu: Add SEEK. 
* gnu/packages/bioinformatics.scm (seek): New variable.
 2016-06-28 22:49:05 +02:00
Ben Woodcroft d6e374a0d9
gnu: mafft: Update to 7.299. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.299.
 2016-06-28 21:42:15 +10:00
Ben Woodcroft 45469ebe52
gnu: metabat: Update to 0.26.3. 
* gnu/packages/bioinformatics.scm (metabat): Update to 0.26.3.
[arguments]: Update include and linking paths accordingly.
 2016-06-28 21:28:06 +10:00
Ben Woodcroft af45244e36
gnu: diamond: Update to 0.8.9. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.9.
 2016-06-28 19:31:25 +10:00
Ben Woodcroft 94ff31572d
gnu: Add khmer. 
* gnu/packages/bioinformatics.scm (khmer): New variable.
* gnu/packages/patches/khmer-use-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-06-27 21:35:16 +10:00
Ben Woodcroft 9ded145717
gnu: Add python-screed. 
* gnu/packages/bioinformatics.scm (python-screed, python2-screed):
New variables.
 2016-06-27 21:16:39 +10:00
Ben Woodcroft c2e575185b
gnu: vsearch: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.0.
 2016-06-26 12:43:39 +10:00
Ben Woodcroft 69af462496
gnu: vsearch: Update to 0.11.2. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 0.11.2.
 2016-06-22 07:51:12 +10:00
Ben Woodcroft 7b3df1e56e
gnu: Add r-vegan. 
* gnu/packages/bioinformatics.scm (r-vegan): New variable.
 2016-06-21 21:29:17 +10:00
Ben Woodcroft cec2653bb4
gnu: diamond: Update to 0.8.7. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.7.
 2016-06-21 20:00:38 +10:00
Ricardo Wurmus 4714d521e3
gnu: Add r-bsgenome-mmusculus-ucsc-mm10. 
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): New
  variable.
 2016-06-15 17:08:08 +02:00
Ben Woodcroft e4a44a6aa5
gnu: Add ruby-bio-kseq. 
* gnu/packages/bioinformatics.scm (ruby-bio-kseq): New variable.
 2016-06-14 07:57:09 +10:00
Ricardo Wurmus 883302daf2
gnu: piranha: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (piranha): Update to 1.2.1.
 2016-06-13 11:53:38 +02:00
Hartmut Goebel 698bd29799
gnu: Use full SHA1 commit ids. 
* gnu/packages/bioinformatics.scm (pbtranscript-tofu, mosaik,
  smithlab-cpp, piranha): Use full SHA1 commit ids.
* gnu/packages/ci.scm (hydra): Likewise.
* gnu/packages/compression.scm (sfarkxtc): Likewise.
* gnu/packages/emacs.scm (emacs-ob-ipython): Likewise.
* gnu/packages/games.scm (mars, emulation-station): Likewise.
* gnu/packages/gnunet.scm (guile-gnunet): Likewise.
* gnu/packages/music.scm (non-sequencer): Likewise.
* gnu/packages/version-control.scm (git-flow, git-test-sequence): Likewise.
* gnu/packages/xorg.scm (xf86-video-intel): Likewise.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-06-05 00:05:38 +02:00
Ben Woodcroft 6ac0a0fbe7
gnu: diamond: Update to 0.8.5. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.5.
 2016-06-04 09:28:54 +10:00
Ricardo Wurmus 64efa3078a
gnu: Add r-genomationdata. 
* gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
 2016-05-31 16:29:37 +02:00
Ben Woodcroft 9fcc3509a7 gnu: Update diamond to 0.8.3. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.3.
 2016-05-28 23:44:16 +10:00
Ricardo Wurmus 0783787436 gnu: Add ParDRe. 
* gnu/packages/bioinformatics.scm (pardre): New variable.
 2016-05-23 12:55:09 +02:00
Ricardo Wurmus 7740f58128
gnu: r-genomation: Update to 1.4.2. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 8ede249e0a
gnu: r-genomicfeatures: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 192e1ea8d1
gnu: r-summarizedexperiment: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus d7420566a9
gnu: r-biocparallel: Update to 1.6.2. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 73af676feb
gnu: r-annotationdbi: Update to 1.34.2. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 679e670b36
gnu: r-variantannotation: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 186ed87337
gnu: r-genomeinfodb: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
 2016-05-20 15:18:23 +02:00
Ben Woodcroft 7c544991dc gnu: diamond: Do not specify target architecture. 
* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not
specify target architecture.
 2016-05-18 21:25:06 +10:00
Ricardo Wurmus e62ffce538 gnu: Add Piranha. 
* gnu/packages/bioinformatics.scm (piranha): New variable.
 2016-05-18 11:59:34 +02:00
Ben Woodcroft 849485f5a0 gnu: sortmerna: Update to 2.1b. 
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b.
[inputs]: New field.
 2016-05-17 21:45:49 +10:00
Ben Woodcroft daaeed765a gnu: vsearch: Update to 1.11.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
 2016-05-17 21:36:46 +10:00
Ben Woodcroft 122395f9fc gnu: diamond: Update to 0.8.1. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1.
[source]: Remove 'snippet'.
[build-system]: Use cmake-build-system.
[arguments]: Remove modifications to phases.
[native-inputs]: Remove field.
[inputs]: Remove 'boost'.
 2016-05-17 21:07:00 +10:00
Ricardo Wurmus 96101b6718
gnu: r-zlibbioc: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0.
 2016-05-16 20:59:50 +02:00
Ricardo Wurmus a0fe3aeecf
gnu: r-motifrg: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0.
 2016-05-16 20:59:38 +02:00
Ricardo Wurmus 1f5786a918
gnu: r-seqlogo: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.38.0.
 2016-05-16 20:59:27 +02:00
Ricardo Wurmus 8adc3b628d
gnu: r-genomation: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.0.
 2016-05-16 20:59:14 +02:00
Ricardo Wurmus 7555817c2b
gnu: r-seqpattern: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.4.0.
 2016-05-16 20:59:04 +02:00
Ricardo Wurmus d1bff89d26
gnu: r-impute: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.46.0.
 2016-05-16 20:58:49 +02:00
Ricardo Wurmus 5190ed1751
gnu: r-bsgenome: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.0.
 2016-05-16 20:58:35 +02:00
Ricardo Wurmus e48e88c217
gnu: r-topgo: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.24.0.
[propagated-inputs]: Add r-matrixstats.
 2016-05-16 20:58:24 +02:00
Ricardo Wurmus 0c56023557
gnu: r-graph: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.50.0.
 2016-05-16 20:58:08 +02:00
Ricardo Wurmus c12b0a5a30
gnu: r-genomicfeatures: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.0.
 2016-05-16 20:57:55 +02:00
Ricardo Wurmus d23fbf1eb9
gnu: r-rtracklayer: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.0.
 2016-05-16 20:57:43 +02:00
Ricardo Wurmus 3cd551ea7b
gnu: r-genomicalignments: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.0.
 2016-05-16 20:57:30 +02:00
Ricardo Wurmus d848ed7cf2
gnu: r-summarizedexperiment: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.0.
 2016-05-16 20:57:21 +02:00
Ricardo Wurmus b4c5a0db22
gnu: r-rsamtools: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.24.0.
 2016-05-16 20:57:10 +02:00
Ricardo Wurmus 2477d9773a
gnu: r-biostrings: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.0.
 2016-05-16 20:56:58 +02:00
Ricardo Wurmus 6a2a0de1ab
gnu: r-biocparallel: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.0.
 2016-05-16 20:56:39 +02:00
Ricardo Wurmus 63cea37234
gnu: r-biomart: Update to 2.28.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.28.0.
 2016-05-16 20:56:29 +02:00
Ricardo Wurmus c4a4e17938
gnu: r-annotationdbi: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.0.
 2016-05-16 20:56:19 +02:00
Ricardo Wurmus 4466a02c9f
gnu: r-biobase: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.32.0.
 2016-05-16 20:56:09 +02:00
Ricardo Wurmus 828980cad6
gnu: r-genomicranges: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.0.
 2016-05-16 20:55:58 +02:00
Ricardo Wurmus e782ca3e97
gnu: r-xvector: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.0.
 2016-05-16 20:55:46 +02:00
Ricardo Wurmus 052ee32b24
gnu: r-variantannotation: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to
  1.18.0.
 2016-05-16 20:55:32 +02:00
Ricardo Wurmus d1ab3d8fa5
gnu: r-genomeinfodb: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.0.
 2016-05-16 20:55:20 +02:00
Ricardo Wurmus 952ff8c862
gnu: r-iranges: Update to 2.6.0. 
* gnu/packages/bioinformatics (r-iranges): Update to 2.6.0.
 2016-05-16 20:55:11 +02:00
Ricardo Wurmus 3654a61146
gnu: r-s4vectors: Update to 0.10.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.0.
 2016-05-16 20:54:59 +02:00
Ricardo Wurmus a936bf59ea
gnu: r-dnacopy: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.46.0.
 2016-05-16 20:54:37 +02:00
Ricardo Wurmus dbfeba5209
gnu: r-biocgenerics: Update to 0.18.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.18.0.
 2016-05-16 20:53:48 +02:00
Efraim Flashner a83e604662
gnu: hmmer: Update urls. 
* gnu/packages/bioinformatics.scm (hmmer)[source]: Project has moved to
eddylab, with their downloads.
[home-page]: Update to new homepage.
 2016-05-16 14:28:53 +03:00
Mark H Weaver 99828fa788
gnu: Update module imports for asciidoc and doxygen. 
This is a followup to commit 0573a923de.

* gnu/packages/algebra.scm, gnu/packages/bioinformatics.scm,
gnu/packages/fcitx.scm, gnu/packages/fish.scm,
gnu/packages/freedesktop.scm, gnu/packages/game-development.scm,
gnu/packages/gcc.scm, gnu/packages/graphics.scm, gnu/packages/image.scm,
gnu/packages/kodi.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/messaging.scm,
gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/rdf.scm,
gnu/packages/serialization.scm, gnu/packages/version-control.scm,
gnu/packages/web.scm, gnu/packages/wm.scm, gnu/packages/xdisorg.scm,
gnu/packages/xiph.scm: Change imports of (gnu packages asciidoc) or
(gnu packages doxygen) to (gnu packages documentation).
 2016-05-12 20:18:15 -04:00
Ricardo Wurmus 83b84fa812 gnu: edirect: Update to 4.10. 
* gnu/packages/bioinformatics.scm (edirect): Update to 4.10.
 2016-05-04 16:45:43 +02:00
Ben Woodcroft 324efb8888 gnu: Add muscle. 
* gnu/packages/bioinformatics.scm (muscle): New variable.
 2016-04-30 15:46:24 +10:00
Ricardo Wurmus fb868e3395 gnu: r-acsnminer: Update to 0.16.01.29. 
* gnu/packages/bioinformatics.scm (r-acsnminer): Update to 0.16.01.29.
 2016-04-26 17:06:17 +02:00
Ricardo Wurmus e1c2ad6777 gnu: r-qtl: Update to 1.39-5. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.39-5.
 2016-04-26 17:06:17 +02:00
Roel Janssen 6b49a37e6b gnu: Add filevercmp. 
* gnu/packages/bioinformatics.scm (filevercmp): New variable.
 2016-04-26 16:41:15 +02:00
Ben Woodcroft 79b555edeb gnu: samtools: Update to 1.3.1. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.1.
 2016-04-24 09:45:07 +10:00
Hartmut Goebel 1ad15c1669 gnu: Rename Java packages to match new naming specification. 
* gnu/packages/bioinformatics.scm (htsjdk): Rename to...
(java-htsjdk): ...this.
(ngs-java): Rename to...
(java-ngs): ...this.
(ncbi-vdb)[arguments,inputs]: Use new name.
* gnu/packages/java.scm (swt): Rename to...
(java-swt): ...this.
* gnu/packages/music.scm (tuxguitar)[make-flags,inputs,arguments]: Use
new name of package "swt".
 2016-04-19 16:55:03 +02:00
Ricardo Wurmus 4d16cc5133 gnu: python2-plastid: Propagate setuptools. 
* gnu/packages/bioinformatics.scm (python2-plastid)[native-inputs]: Move
python2-setuptools from here...
[propagated-inputs]: ...to here.
 2016-04-19 16:12:51 +02:00
Ricardo Wurmus f94bf1983b gnu: Add python-plastid. 
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New
  variables.
 2016-04-19 12:16:01 +02:00
Ricardo Wurmus 4db9433aa0 gnu: Add python-twobitreader. 
* gnu/packages/bioinformatics.scm (python-twobitreader,
  python2-twobitreader): New variables.
 2016-04-19 12:16:01 +02:00
Alex Kost fc1adab148 gnu: packages: Use 'search-patches' everywhere. 
* gnu/packages/abiword.scm: Use 'search-patches' for 'patches' field.
* gnu/packages/acl.scm: Likewise.
* gnu/packages/admin.scm: Likewise.
* gnu/packages/algebra.scm: Likewise.
* gnu/packages/animation.scm: Likewise.
* gnu/packages/apr.scm: Likewise.
* gnu/packages/audacity.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/autotools.scm: Likewise.
* gnu/packages/avahi.scm: Likewise.
* gnu/packages/backup.scm: Likewise.
* gnu/packages/base.scm: Likewise.
* gnu/packages/bash.scm: Likewise.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/ci.scm: Likewise.
* gnu/packages/cmake.scm: Likewise.
* gnu/packages/cpio.scm: Likewise.
* gnu/packages/cross-base.scm: Likewise.
* gnu/packages/dico.scm: Likewise.
* gnu/packages/doxygen.scm: Likewise.
* gnu/packages/ebook.scm: Likewise.
* gnu/packages/elf.scm: Likewise.
* gnu/packages/emacs.scm: Likewise.
* gnu/packages/engineering.scm: Likewise.
* gnu/packages/firmware.scm: Likewise.
* gnu/packages/flashing-tools.scm: Likewise.
* gnu/packages/fltk.scm: Likewise.
* gnu/packages/ftp.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gawk.scm: Likewise.
* gnu/packages/gcc.scm: Likewise.
* gnu/packages/gd.scm: Likewise.
* gnu/packages/ghostscript.scm: Likewise.
* gnu/packages/glib.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/gnucash.scm: Likewise.
* gnu/packages/gnunet.scm: Likewise.
* gnu/packages/gnupg.scm: Likewise.
* gnu/packages/gnuzilla.scm: Likewise.
* gnu/packages/graphics.scm: Likewise.
* gnu/packages/grub.scm: Likewise.
* gnu/packages/gtk.scm: Likewise.
* gnu/packages/guile.scm: Likewise.
* gnu/packages/icu4c.scm: Likewise.
* gnu/packages/idutils.scm: Likewise.
* gnu/packages/image.scm: Likewise.
* gnu/packages/imagemagick.scm: Likewise.
* gnu/packages/irc.scm: Likewise.
* gnu/packages/ldc.scm: Likewise.
* gnu/packages/libcanberra.scm: Likewise.
* gnu/packages/libevent.scm: Likewise.
* gnu/packages/libreoffice.scm: Likewise.
* gnu/packages/libunwind.scm: Likewise.
* gnu/packages/libusb.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/lirc.scm: Likewise.
* gnu/packages/llvm.scm: Likewise.
* gnu/packages/lsh.scm: Likewise.
* gnu/packages/lua.scm: Likewise.
* gnu/packages/lxqt.scm: Likewise.
* gnu/packages/mail.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mcrypt.scm: Likewise.
* gnu/packages/messaging.scm: Likewise.
* gnu/packages/mit-krb5.scm: Likewise.
* gnu/packages/mp3.scm: Likewise.
* gnu/packages/multiprecision.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/ninja.scm: Likewise.
* gnu/packages/nvi.scm: Likewise.
* gnu/packages/ocaml.scm: Likewise.
* gnu/packages/orpheus.scm: Likewise.
* gnu/packages/ots.scm: Likewise.
* gnu/packages/parallel.scm: Likewise.
* gnu/packages/patchutils.scm: Likewise.
* gnu/packages/pcre.scm: Likewise.
* gnu/packages/pdf.scm: Likewise.
* gnu/packages/perl.scm: Likewise.
* gnu/packages/plotutils.scm: Likewise.
* gnu/packages/polkit.scm: Likewise.
* gnu/packages/pulseaudio.scm: Likewise.
* gnu/packages/python.scm: Likewise.
* gnu/packages/qemu.scm: Likewise.
* gnu/packages/qt.scm: Likewise.
* gnu/packages/ratpoison.scm: Likewise.
* gnu/packages/rdf.scm: Likewise.
* gnu/packages/readline.scm: Likewise.
* gnu/packages/rush.scm: Likewise.
* gnu/packages/scheme.scm: Likewise.
* gnu/packages/screen.scm: Likewise.
* gnu/packages/sdl.scm: Likewise.
* gnu/packages/slim.scm: Likewise.
* gnu/packages/ssh.scm: Likewise.
* gnu/packages/tcl.scm: Likewise.
* gnu/packages/tcsh.scm: Likewise.
* gnu/packages/texinfo.scm: Likewise.
* gnu/packages/tls.scm: Likewise.
* gnu/packages/tor.scm: Likewise.
* gnu/packages/tv.scm: Likewise.
* gnu/packages/valgrind.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/vpn.scm: Likewise.
* gnu/packages/vtk.scm: Likewise.
* gnu/packages/w3m.scm: Likewise.
* gnu/packages/web.scm: Likewise.
* gnu/packages/wicd.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xfce.scm: Likewise.
* gnu/packages/xiph.scm: Likewise.
* gnu/packages/xml.scm: Likewise.
* gnu/packages/xorg.scm: Likewise.
* gnu/packages/zip.scm: Likewise.
 2016-04-14 10:38:21 +03:00
Ricardo Wurmus 6dc6099853 gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3. 
* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3):
  New variable.
 2016-04-11 15:11:16 +02:00
Ricardo Wurmus 943bd6279f gnu: Add r-bsgenome-celegans-ucsc-ce6. 
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): New
  variable.
 2016-04-11 15:11:16 +02:00
Ricardo Wurmus a3e9028770 gnu: Add r-bsgenome-mmusculus-ucsc-mm9. 
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): New
  variable.
 2016-04-11 15:11:15 +02:00
Ricardo Wurmus ae2462f7dd gnu: Add r-motifrg. 
* gnu/packages/bioinformatics.scm (r-motifrg): New variable.
 2016-04-11 11:03:27 +02:00
Ricardo Wurmus c90a4baff6 gnu: Add r-bsgenome-hsapiens-ucsc-hg19. 
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): New
  variable.
 2016-04-11 11:03:27 +02:00
Ricardo Wurmus 936e7d6774 gnu: Add r-seqlogo. 
* gnu/packages/bioinformatics.scm (r-seqlogo): New variable.
 2016-04-11 11:03:27 +02:00
Roel Janssen 9e3ba31c53 gnu: Add r-zlibbioc. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-04-06 17:38:42 -04:00
Roel Janssen b669d9c4c8 gnu: Add r-variantannotation. 
* gnu/packages/bioinformatics.scm (r-variantannotation): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-04-06 17:38:42 -04:00
Roel Janssen 9b36e25607 gnu: vcftools: Update to 0.1.14. 
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.14.
[arguments]: Do not modify phases as it is not needed anymore.
[native-inputs]: Add 'pkg-config'.
[home-page]: Update to new location.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-04-05 11:29:32 +03:00
Efraim Flashner ddb8312911 gnu: python2-pbcore: Update to 1.2.8. 
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.8.
[native-inputs]: Add python2-docutils, python2-nose, python2-sphinx.
 2016-03-30 22:45:35 +03:00
Ricardo Wurmus f315f4fcab gnu: r-genomation: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.2.2.
 2016-03-30 11:59:16 +02:00
Ricardo Wurmus 571f0b63d5 gnu: r-genomicfeatures: Update to 1.22.13. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to
  1.22.13.
 2016-03-30 11:59:16 +02:00
Ricardo Wurmus ffaf72ad96 gnu: r-rtracklayer: Update to 1.30.4. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.30.4.
 2016-03-30 11:59:15 +02:00
Ricardo Wurmus ac2d8b0fb8 gnu: r-genomicalignments: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to
  1.6.3.
 2016-03-30 11:59:15 +02:00
Ricardo Wurmus 7eade1c5f9 gnu: r-summarizedexperiment: Update to 1.0.2. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to
  1.0.2.
 2016-03-30 11:59:15 +02:00
Ricardo Wurmus 53fd0f5e1d gnu: r-biostrings: Update to 2.38.4. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.38.4.
 2016-03-30 11:59:15 +02:00
Ricardo Wurmus 5fe3115415 gnu: r-genomicranges: Update to 1.22.4. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.22.4.
 2016-03-30 11:59:15 +02:00
Ricardo Wurmus 9cc22d28d8 gnu: r-genomeinfodb: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.6.3.
 2016-03-30 11:59:15 +02:00
Ricardo Wurmus 1d216b6ec9 gnu: Remove "r-repository" property. 
* gnu/packages/bioinformatics.scm (r-biocgenerics, r-s4vectors,
r-iranges, r-genomeinfodb, r-xvector, r-genomicranges)[properties]:
Remove "r-repository" property.
 2016-03-24 16:18:01 +01:00
Ludovic Courtès 5697fdc366 gnu: r-dnacopy: Fix home page URL. 
* gnu/packages/bioinformatics.scm (r-dnacopy)[home-page]: Add missing
URI scheme.
 2016-03-18 23:00:04 +01:00
Ricardo Wurmus 953c12232f gnu: bless: Remove bundled sources for sparsehash. 
* gnu/packages/bioinformatics.scm (bless)[source]: Delete
"google-sparsehash" sources.
[inputs]: Add "sparsehash".
 2016-03-17 13:01:31 +01:00
Ricardo Wurmus 6c1305f9ec gnu: Add CD-HIT. 
* gnu/packages/bioinformatics.scm (cd-hit): New variable.
 2016-03-17 13:01:31 +01:00