| Age | Commit message (Expand) | Author |
|---|
| 2016-12-27 | gnu: r-rcas: Update to 1.1.1....* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.1.1.
[propagated-inputs]: Add plotrix.
| Ricardo Wurmus |
| 2016-12-27 | gnu: diamond: Update to 0.8.30....* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.30.
| Ben Woodcroft |
| 2016-12-20 | gnu: cutadapt: Use ‘modify-phases’ syntax....* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Use
‘modify-phases’.
| Tobias Geerinckx-Rice |
| 2016-12-19 | gnu: cutadapt: Update to 1.12....* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.12.
[inputs]: Add python-xopen.
| Tobias Geerinckx-Rice |
| 2016-12-18 | gnu: Add attribution line for Raoul Bonnal....This is a follow-up commit to c9e9154e993f055a438e2e43518bbd0740aaaf24.
* gnu/packages/bioinformatics.scm: Add attribution.
| Ben Woodcroft |
| 2016-12-17 | 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>
| Raoul Bonnal |
| 2016-12-14 | gnu: Update more dead Google Code home pages....* gnu/packages/bioinformatics.scm (cutadapt, mosaik, pepr)[home-page]:
Update to their respective replacements.
| Tobias Geerinckx-Rice |
| 2016-12-13 | gnu: diamond: Update to 0.8.29....* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.29.
| Ben Woodcroft |
| 2016-12-13 | gnu: orfm: Update to 0.6.1....* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.1.
| Ben Woodcroft |
| 2016-12-12 | gnu: orfm: Update to 0.6.0....* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.0.
| Ben Woodcroft |
| 2016-12-10 | gnu: vsearch: Update to 2.3.4....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.4.
| Ben Woodcroft |
| 2016-12-10 | gnu: pardre: Update to 1.1.5-1....* gnu/packages/bioinformatics.scm (pardre): update to 1.1.5-1.
[source]: Update source hash.
| Ben Woodcroft |
| 2016-12-08 | gnu: vsearch: Update to 2.3.3....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.3.
| Ben Woodcroft |
| 2016-12-04 | gnu: aragorn: Update to 1.2.38....* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.38.
| Ben Woodcroft |
| 2016-11-29 | Merge branch 'master' into python-build-system | Hartmut Goebel |
| 2016-11-28 | gnu: Add r-gkmsvm....* gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
| Ricardo Wurmus |
| 2016-11-28 | gnu: Add r-seqgl....* gnu/packages/bioinformatics.scm (r-seqgl): New variable.
| Ricardo Wurmus |
| 2016-11-28 | gnu: Add r-chipkernels....* gnu/packages/bioinformatics.scm (r-chipkernels): New variable.
| Ricardo Wurmus |
| 2016-11-28 | gnu: Add r-wgcna....* gnu/packages/bioinformatics.scm (r-wgcna): New variable.
| Ricardo Wurmus |
| 2016-11-28 | gnu: Add r-r4rna....* gnu/packages/bioinformatics.scm (r-r4rna): New variable.
| Ricardo Wurmus |
| 2016-11-28 | gnu: Add newick-utils....* gnu/packages/bioinformatics.scm (newick-utils): New variable.
| Ben Woodcroft |
| 2016-11-26 | gnu: roary: Update to 3.7.0....* gnu/packages/bioinformatics.scm (roary): Update to 3.7.0.
| Ben Woodcroft |
| 2016-11-26 | gnu: Add proteinortho....* gnu/packages/bioinformatics.scm (proteinortho): New variable.
| Ben Woodcroft |
| 2016-11-25 | Merge branch 'master' into python-build-system | Leo Famulari |
| 2016-11-22 | gnu: diamond: Update to 0.8.27....* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27.
| Ben Woodcroft |
| 2016-11-21 | gnu: Remove redundancy where mkdir-p <dir> is followed by install-file <file>......* 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>
| Petter |
| 2016-11-15 | 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].
| Hartmut Goebel |
| 2016-11-15 | 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.
| Hartmut Goebel |
| 2016-11-15 | 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.
| Hartmut Goebel |
| 2016-11-15 | 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
| Hartmut Goebel |
| 2016-11-15 | 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.
| Hartmut Goebel |
| 2016-11-15 | 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.
| Hartmut Goebel |
| 2016-11-15 | 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.
| Hartmut Goebel |
| 2016-11-15 | 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.
| Hartmut Goebel |
| 2016-11-15 | 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.
| Hartmut Goebel |
| 2016-11-15 | gnu: hisat: Fix typo....* gnu/packages/bioinformatics.scm (hisat)[arguments]: Fix directory
name in install phase.
| Ricardo Wurmus |
| 2016-11-11 | 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.
| Ricardo Wurmus |
| 2016-11-11 | 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.
| Ricardo Wurmus |
| 2016-11-11 | 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.
| Ricardo Wurmus |
| 2016-11-11 | 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.
| Ricardo Wurmus |
| 2016-11-07 | gnu: diamond: Update to 0.8.26....* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.26.
| Ben Woodcroft |
| 2016-11-03 | gnu: r-rcas: Update to 1.0.0....* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.0.0.
| Ricardo Wurmus |
| 2016-11-03 | gnu: r-rtracklayer: Update to 1.34.1....* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.1.
| Ricardo Wurmus |
| 2016-11-03 | gnu: r-biocparallel: Update to 1.8.1....* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.1.
| Ricardo Wurmus |
| 2016-11-03 | gnu: r-limma: Update to 3.30.2....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.2.
| Ricardo Wurmus |
| 2016-11-03 | gnu: r-edger: Update to 3.16.1....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.1.
| Ricardo Wurmus |
| 2016-10-28 | gnu: python-twobitreader: Update to 3.1.4....* gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader):
Update to 3.1.4.
| Leo Famulari |
| 2016-10-28 | 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.
| Leo Famulari |
| 2016-10-27 | gnu: Add r-mutationalpatterns....* gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
| Roel Janssen |
| 2016-10-26 | gnu: r-seqinr: Update to 3.3-3....* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-3.
| Ricardo Wurmus |
