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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
7500e42b3e
gnu: Add r-mutationalpatterns.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
2016-10-27 20:07:05 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
4644644ace
gnu: Add r-bioccheck.
...
* gnu/packages/bioinformatics.scm (r-bioccheck): New variable.
2016-10-20 09:53:02 +02:00
99df12cd19
gnu: Add r-biocstyle.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): New variable.
2016-10-19 15:22:06 +02:00
207ce8fbe5
gnu: Add r-biocviews.
...
* gnu/packages/bioinformatics.scm (r-biocviews): New variable.
2016-10-19 15:09:55 +02:00
c79ad57a8d
gnu: Add r-optparse.
...
* gnu/packages/bioinformatics.scm (r-optparse): New variable.
2016-10-19 10:48:56 +02:00
2acaaee550
gnu: Add r-getopt.
...
* gnu/packages/bioinformatics.scm (r-getopt): New variable.
2016-10-19 09:55:45 +02:00
5093729704
gnu: Add rcas-web.
...
* gnu/packages/bioinformatics.scm (rcas-web): New variable.
2016-10-17 18:09:20 +02:00
89984be46e
gnu: Add r-rcas.
...
* gnu/packages/bioinformatics.scm (r-rcas): New variable.
2016-10-17 18:09:16 +02:00
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
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
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
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
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
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
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
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
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
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
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
bdc7be59eb
gnu: Add bcftools.
...
* gnu/packages/bioinformatics.scm (bcftools): New variable.
2016-09-27 20:06:00 +10:00
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
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
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
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
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
684f29bd2e
gnu: Add r-grohmm.
...
* gnu/packages/bioinformatics.scm (r-grohmm): New variable.
2016-09-26 07:47:55 +02:00
7f903d7300
gnu: Add r-systempiper.
...
* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
2016-09-26 07:47:55 +02:00
cb99d457f0
gnu: Add r-shortread.
...
* gnu/packages/bioinformatics.scm (r-shortread): New variable.
2016-09-26 07:47:54 +02:00
89f40c5e4e
gnu: Add r-gostats.
...
* gnu/packages/bioinformatics.scm (r-gostats): New variable.
2016-09-26 07:47:54 +02:00
1a1931f7e0
gnu: Add r-category.
...
* gnu/packages/bioinformatics.scm (r-category): New variable.
2016-09-26 07:47:54 +02:00
ad740ff818
gnu: Add r-gseabase.
...
* gnu/packages/bioinformatics.scm (r-gseabase): New variable.
2016-09-26 07:47:53 +02:00
cd9e7dc7ff
gnu: Add r-rbgl.
...
* gnu/packages/bioinformatics.scm (r-rbgl): New variable.
2016-09-26 03:25:23 +02:00
e816377374
gnu: Add r-annotationforge.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): New variable.
2016-09-26 03:25:17 +02:00
ad34f0ac96
gnu: Add r-deseq2.
...
* gnu/packages/bioinformatics.scm (r-deseq2): New variable.
2016-09-26 03:21:27 +02:00
2301fd3e4d
gnu: Add r-genefilter.
...
* gnu/packages/bioinformatics.scm (r-genefilter): New variable.
2016-09-26 03:21:19 +02:00
07a664cde0
gnu: Add r-geneplotter.
...
* gnu/packages/bioinformatics.scm (r-geneplotter): New variable.
2016-09-26 03:21:07 +02:00
Hartmut Goebel