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
