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path: root/gnu/packages/bioinformatics.scm
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2016-12-04gnu: aragorn: Update to 1.2.38.Ben Woodcroft
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.38.
2016-11-29Merge branch 'master' into python-build-systemHartmut Goebel
2016-11-28gnu: Add r-gkmsvm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
2016-11-28gnu: Add r-seqgl.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqgl): New variable.
2016-11-28gnu: Add r-chipkernels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-chipkernels): New variable.
2016-11-28gnu: Add r-wgcna.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-wgcna): New variable.
2016-11-28gnu: Add r-r4rna.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-r4rna): New variable.
2016-11-28gnu: Add newick-utils.Ben Woodcroft
* gnu/packages/bioinformatics.scm (newick-utils): New variable.
2016-11-26gnu: roary: Update to 3.7.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (roary): Update to 3.7.0.
2016-11-26gnu: Add proteinortho.Ben Woodcroft
* gnu/packages/bioinformatics.scm (proteinortho): New variable.
2016-11-25Merge branch 'master' into python-build-systemLeo Famulari
2016-11-22gnu: diamond: Update to 0.8.27.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27.
2016-11-21gnu: Remove redundancy where mkdir-p <dir> is followed by install-file ↵Petter
<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>
2016-11-15gnu: python2-pbcore: Fix inputs:Hartmut Goebel
* 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].
2016-11-15gnu: python2-warpedlmm: Remove phase remove-bin-directory.Hartmut Goebel
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.
2016-11-15gnu: Fix python inputs, part 7: Ensure python-cython is a native-input.Hartmut Goebel
* 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.
2016-11-15gnu: Fix python inputs, part 1: all inputs become propagated-inputs.Hartmut Goebel
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
2016-11-15gnu: Remove work-arounds for bug 20765 (ensure uncompressed eggs).Hartmut Goebel
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.
2016-11-15gnu: Remove python-setuptools and python2-setuptools from inputs (part 4a)Hartmut Goebel
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.
2016-11-15gnu: Remove python-setuptools and python2-setuptools from inputs (part 3)Hartmut Goebel
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.
2016-11-15gnu: Remove python-setuptools and python2-setuptools from inputs (part 2)Hartmut Goebel
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.
2016-11-15gnu: Remove python-setuptools and python2-setuptools from inputs (part 1b)Hartmut Goebel
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.
2016-11-15gnu: hisat: Fix typo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Fix directory name in install phase.
2016-11-11gnu: r-org-mm-eg-db: Update to 3.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.4.0.
2016-11-11gnu: r-org-dm-eg-db: Update to 3.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.4.0.
2016-11-11gnu: r-org-ce-eg-db: Update to 3.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.4.0.
2016-11-11gnu: r-org-hs-eg-db: Update to 3.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.4.0.
2016-11-07gnu: diamond: Update to 0.8.26.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.26.
2016-11-03gnu: r-rcas: Update to 1.0.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.0.0.
2016-11-03gnu: r-rtracklayer: Update to 1.34.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.1.
2016-11-03gnu: r-biocparallel: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.1.
2016-11-03gnu: r-limma: Update to 3.30.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.2.
2016-11-03gnu: r-edger: Update to 3.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.1.
2016-10-28gnu: python-twobitreader: Update to 3.1.4.Leo Famulari
* gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader): Update to 3.1.4.
2016-10-28gnu: python-twobitreader: Disable the test suite.Leo Famulari
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.
2016-10-27gnu: Add r-mutationalpatterns.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
2016-10-26gnu: r-seqinr: Update to 3.3-3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-3.
2016-10-26gnu: bioperl-minimal: Update to 1.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bioperl-minimal): Update to 1.7.0.
2016-10-26gnu: r-genomationdata: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.6.0.
2016-10-26gnu: r-bamsignals: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.6.0.
2016-10-26gnu: r-rhtslib: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.6.0. [native-inputs]: Add autoconf.
2016-10-26gnu: r-zlibbioc: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.20.0.
2016-10-26gnu: r-motifrg: Update to 1.18.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.18.0.
2016-10-26gnu: r-seqlogo: Update to 1.40.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.40.0.
2016-10-26gnu: r-genomation: Update to 1.6.0.Ricardo Wurmus
* 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.
2016-10-26gnu: r-seqpattern: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.6.0. [propagated-inputs]: Add r-kernsmooth.
2016-10-26gnu: r-impute: Update to 1.48.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.48.0.
2016-10-26gnu: r-bsgenome: Update to 1.42.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.42.0.
2016-10-26gnu: r-topgo: Update to 2.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0. [propagated-inputs]: Add r-dbi.
2016-10-26gnu: r-graph: Update to 1.52.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0.
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