Mark H Weaver
1a265842e6
gnu: Use PACKAGE/INHERIT in more places.
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* gnu/packages/algebra.scm (fftwf, fftw-openmpi),
gnu/packages/audio.scm (ztoolkit-rsvg),
gnu/packages/bioinformatics.scm (python2-dendropy),
gnu/packages/boost.scm (boost-with-python2),
gnu/packages/check.scm (python2-mock, python2-pytest-mock),
gnu/packages/cups.scm (hplip-minimal),
gnu/packages/freedesktop.scm (libinput-minimal),
gnu/packages/gettext.scm (gnu-gettext),
gnu/packages/glib.scm (python2-pygobject),
gnu/packages/gnome.scm (gdl-minimal, libsoup-minimal, python2-pyatspi),
gnu/packages/groff.scm (groff-minimal),
gnu/packages/jami.scm (ffmpeg-jami),
gnu/packages/libcanberra.scm (libcanberra/gtk+-2),
gnu/packages/lirc.scm (python2-lirc),
gnu/packages/llvm.scm (clang-runtime-3.5),
gnu/packages/mpi.scm (java-openmpi, openmpi-thread-multiple),
gnu/packages/node.scm (libnode),
gnu/packages/onc-rpc.scm (libtirpc/hurd),
gnu/packages/python-compression.scm (bitshuffle-for-snappy),
gnu/packages/python-crypto.scm (python2-pycrypto, python2-cryptography)
(python2-cryptography, python2-m2crypto),
gnu/packages/python-web.scm (python2-html2text, python2-tornado)
(python2-terminado, python2-ndg-httpsclient, python2-websocket-client)
(python2-rauth, python2-url, python2-s3transfer),
gnu/packages/python-xyz.scm (python2-psutil, python2-serpent)
(python2-humanfriendly, python2-empy, python2-parse-type, python2-polib)
(python2-jsonschema, python2-pystache, python2-cython, python2-numpydoc)
(python2-ipyparallel, python2-traitlets, python2-dbus)
(python2-beautifulsoup4, python2-pep517, python2-flake8, python2-llfuse)
(python2-tlsh, python-file, python2-notebook, python-jupyter-console-minimal)
(python2-contextlib2, python2-promise, python2-anyjson, python2-amqp)
(python2-kombu, python2-billiard, python2-celery, python2-whoosh)
(python2-jellyfish, python-rope, ptpython-2, python2-binaryornot)
(python2-setproctitle, python2-argcomplete, python2-xopen, python2-isort)
(python2-radon, python2-rfc6555, python2-activepapers, python2-send2trash)
(python2-cloudpickle, python2-reparser),
gnu/packages/python.scm (python2-called-python),
gnu/packages/qt.scm (python2-sip, python-pyqt-without-qtwebkit, python2-pyqt)
(python-qscintilla, python-pyqt+qscintilla),
gnu/packages/scanner.scm (sane-backends),
gnu/packages/sdl.scm (guile3.0-sdl2),
gnu/packages/selinux.scm (checkpolicy, libselinux, libsemanage, secilc)
(python-sepolgen, policycoreutils),
gnu/packages/serialization.scm (lua5.1-libmpack, lua5.2-libmpack),
gnu/packages/simulation.scm (fenics),
gnu/packages/statistics.scm (python2-statsmodels),
gnu/packages/texinfo.scm (info-reader),
gnu/packages/wxwidgets.scm (wxwidgets-gtk2, wxwidgets-gtk2-3.1),
gnu/packages/xml.scm (xmlsec-nss),
gnu/packages/xorg.scm (uim-gtk, uim-qt),
guix/build-system/python.scm (package-with-explicit-python)
(strip-python2-variant): Use PACKAGE/INHERIT.
2021-03-17 03:58:10 -04:00
Ricardo Wurmus
fcf8c6c565
gnu: hisat2: Update to 2.2.1.
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* gnu/packages/bioinformatics.scm (hisat2): Update to 2.2.1.
[source]: Fetch from git repository on Github.
[arguments]: Add phase to build manual; remove trailing #t from other phases.
[native-inputs]: Remove unzip.
[home-page]: Update.
[inputs]: Add python-wrapper.
2021-03-16 11:12:01 +01:00
Leo Famulari
8ec0ca8faf
Revert some commits that caused guix pull to fail.
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This reverts commits 821e6439218f9fd9b70c
2021-03-15 19:52:34 -04:00
zimoun
d99a18252c
gnu: r-delayedarray: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here...
* gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
adf45daae9
gnu: r-rsamtools: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
b1a19ab6e2
gnu: r-biostrings: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-biostrings): Move from here...
* gnu/packages/bioconductor.scm (r-biostrings): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
eab9807fb3
gnu: r-biocparallel: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here...
* gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
c11b541fba
gnu: r-biomart: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-biomart): Move from here...
* gnu/packages/bioconductor.scm (r-biomart): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
16c7e79ebb
gnu: r-annotationdbi: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here...
* gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
457de7f401
gnu: r-biobase: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-biobase): Move from here...
* gnu/packages/bioconductor.scm (r-biobase): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
f3f09b99cd
gnu: r-genomicranges: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here...
* gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
e56b3db82e
gnu: r-xvector: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-xvector): Move from here...
* gnu/packages/bioconductor.scm (r-xvector): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
821e643921
gnu: r-limma: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-limma): Move from here...
* gnu/packages/bioconductor.scm (r-limma): ...to here.
2021-03-15 23:30:26 +01:00
Ricardo Wurmus
14204d696c
gnu: r-genomicfeatures: Update to 1.42.2.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2.
2021-03-15 15:03:08 +01:00
Ricardo Wurmus
f10f2745eb
gnu: r-delayedarray: Update to 0.16.2.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2.
2021-03-15 15:03:08 +01:00
zimoun
bf612ead76
gnu: r-variantannotation: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-variantannotation): Move from here...
* gnu/packages/bioconductor.scm (r-variantannotation): ...to here.
2021-03-15 14:06:24 +01:00
zimoun
082f3c5433
gnu: r-edger: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-edger): Move from here...
* gnu/packages/bioconductor.scm (r-edger): ...to here.
2021-03-15 14:06:16 +01:00
zimoun
35b62c044e
gnu: r-genomeinfodb: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here.
2021-03-15 14:05:56 +01:00
zimoun
8d6d75ff39
gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here.
[source]: Use 'bioconductor-uri'.
2021-03-15 14:05:47 +01:00
zimoun
9949f459bf
gnu: r-iranges: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-iranges): Move from here...
* gnu/packages/bioconductor.scm (r-iranges): ...to here.
2021-03-15 14:05:37 +01:00
zimoun
d64e3a487b
gnu: r-s4vectors: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-s4vectors): Move from here...
* gnu/packages/bioconductor.scm (r-s4vectors): ...to here.
2021-03-15 14:05:27 +01:00
zimoun
852fa82d4c
gnu: r-bioccheck: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-bioccheck): Move from here...
* gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
2021-03-15 14:05:22 +01:00
zimoun
d5576b6eb7
gnu: r-grohmm: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-grohmm): Move from here...
* gnu/packages/bioconductor.scm (r-grohmm): ...to here.
2021-03-15 14:04:26 +01:00
zimoun
5ac55aea8b
gnu: r-biocstyle: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-biocstyle): Move from here...
* gnu/packages/bioconductor.scm (r-biocstyle): ...to here.
2021-03-15 14:03:21 +01:00
zimoun
134404b437
gnu: r-biocviews: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-biocviews): Move from here...
* gnu/packages/bioconductor.scm (r-biocviews): ...to here.
2021-03-15 14:03:18 +01:00
Ricardo Wurmus
6e0ed09e68
gnu: Add instrain.
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* gnu/packages/bioinformatics.scm (instrain): New variable.
2021-03-15 11:43:20 +01:00
Ricardo Wurmus
ad34eb222c
gnu: Add python-drep.
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* gnu/packages/bioinformatics.scm (python-drep): New variable.
2021-03-15 11:43:20 +01:00
zimoun
df6b3c25bb
gnu: r-systempiper: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-systempiper): Move from here...
* gnu/packages/bioconductor.scm (r-systempiper): ...to here.
2021-03-12 14:45:55 +01:00
zimoun
8957efa8ef
gnu: r-shortread: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
2021-03-12 14:45:54 +01:00
zimoun
2a97057688
gnu: r-gostats: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-gostats): Move from here...
* gnu/packages/bioconductor.scm (r-gostats): ...to here.
2021-03-12 14:45:54 +01:00
zimoun
4e7cf96c9f
gnu: r-category: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-category): Move from here...
* gnu/packages/bioconductor.scm (r-category): ...to here.
2021-03-12 14:45:54 +01:00
zimoun
031fdda47a
gnu: r-gseabase: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-gseabase): Move from here...
* gnu/packages/bioconductor.scm (r-gseabase): ...to here.
2021-03-12 14:45:54 +01:00
zimoun
f44079bc21
gnu: r-rbgl: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-rbgl): Move from here...
* gnu/packages/bioconductor.scm (r-rbgl): ...to here.
2021-03-12 14:45:54 +01:00
zimoun
ff92c2873c
gnu: r-annotationforge: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-annotationforge): Move from here...
* gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
2021-03-12 14:45:53 +01:00
zimoun
d769b10714
gnu: r-dexseq: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-dexseq): Move from here...
* gnu/packages/bioconductor.scm (r-dexseq): ...to here.
2021-03-12 14:45:53 +01:00
zimoun
373545855d
gnu: r-deseq2: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-deseq2): Move from here...
* gnu/packages/bioconductor.scm (r-deseq2): ...to here.
2021-03-12 14:45:53 +01:00
zimoun
a35ea5fed9
gnu: r-genefilter: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-genefilter): Move from here...
* gnu/packages/bioconductor.scm (r-genefilter): ...to here.
2021-03-12 14:45:53 +01:00
Efraim Flashner
5ae7414860
gnu: Add bandage.
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* gnu/packages/bioinformatics.scm (bandage): New variable.
2021-03-11 16:54:38 +02:00
Ricardo Wurmus
133a918923
gnu: trim-galore: Update to 0.6.6.
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* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.6.
2021-03-09 11:54:59 +01:00
Ricardo Wurmus
49d85b3f11
gnu: bbmap: Update to 38.90.
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* gnu/packages/bioinformatics.scm (bbmap): Update to 38.90.
2021-03-09 11:54:59 +01:00
Nicolas Goaziou
ea8e89292c
gnu: seqan-1: Use HTTPS source URI.
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* gnu/packages/bioinformatics.scm (seqan-1)[source]: Use HTTPS URI.
2021-03-06 16:05:44 +01:00
Nicolas Goaziou
e062572812
gnu: seqan: Use HTTPS home page URI.
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* gnu/packages/bioinformatics.scm (seqan)[home-page]: Use HTTPS URI.
2021-03-06 16:01:24 +01:00
Ricardo Wurmus
f5c3e8e2ec
gnu: Add r-cellchat.
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* gnu/packages/bioinformatics.scm (r-cellchat): New variable.
2021-03-05 15:04:15 +01:00
Tim Howes
dcee10506c
gnu: infernal: Update to 1.1.4.
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* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.4.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-03-03 10:11:51 +02:00
Tim Howes
9f4ffc249f
gnu: hmmer: Update to 3.3.2.
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* gnu/packages/bioinformatics.scm (hmmer): Update to 3.3.2.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-03-03 10:11:51 +02:00
Ricardo Wurmus
f21c711a0f
gnu: kallisto: Update to 0.46.2.
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* gnu/packages/bioinformatics.scm (kallisto): Update to 0.46.2.
[source]: Remove bundled htslib sources.
2021-03-02 17:06:58 +01:00
Ricardo Wurmus
cc39e9dbdc
gnu: kallisto: Use older htslib.
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* gnu/packages/bioinformatics.scm (kallisto)[inputs]: Use htslib-1.9 instead
of the latest.
2021-03-02 17:06:58 +01:00
Nicolas Goaziou
3759df574d
gnu: f-seq: Use HTTPS home page URI.
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* gnu/packages/bioinformatics.scm (f-seq)[home-page]: Use HTTPS URI.
2021-02-28 11:03:56 +01:00
Ricardo Wurmus
5d5bbd6fcc
gnu: Add star-for-pigx.
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This is a follow-up to commit f1f6e49190
2021-02-23 19:40:59 +01:00
Ricardo Wurmus
f1f6e49190
gnu: star: Update to 2.7.8a.
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* gnu/packages/bioinformatics.scm (star): Update to 2.7.8a.
2021-02-22 21:16:19 +01:00
