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Author SHA1 Message Date
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
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
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