e740cc6140
Merge branch 'master' into core-updates
2021-02-03 09:57:35 +00:00
877ab0266c
gnu: vcflib: Fix generated pkg-config file.
...
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In custom
generated pkg-config file, link with all needed libraries and
fix linker library.
* gnu/packages/patches/freebayes-devendor-deps.patch: Adjust accordingly.
2021-02-01 19:02:14 +02:00
d42245d401
gnu: Adjust package collection to Wrap using GUIX_PYTHONPATH.
...
This change was automated using:
$ git ls-files | grep .scm | \
xargs sed 's/(getenv "PYTHONPATH")/(getenv "GUIX_PYTHONPATH")/' -i
$ git ls-files | grep .scm | \
xargs sed 's/`("PYTHONPATH"/`("GUIX_PYTHONPATH"/' -i
* gnu/packages/admin.scm (nmap):
(dstat): Wrap using GUIX_PYTHONPATH.
* gnu/packages/audio.scm (jack-2):
(carla): Likewise.
* gnu/packages/benchmark.scm (fio): Likewise.
* gnu/packages/bioinformatics.scm (couger): Likewise.
(gess, find-circ, filtlong, nanopolish): Likewise.
* gnu/packages/cdrom.scm (cdemu-client): Likewise.
* gnu/packages/chemistry.scm (avogadro): Likewise.
* gnu/packages/connman.scm (econnman): Likewise.
* gnu/packages/cups.scm (hplip): Likewise.
* gnu/packages/debug.scm (scanmem): Likewise.
* gnu/packages/display-managers.scm (lightdm): Likewise.
* gnu/packages/ebook.scm (cozy): Likewise.
* gnu/packages/education.scm (anki): Likewise.
* gnu/packages/engineering.scm (kicad, volk, freecad): Likewise.
* gnu/packages/game-development.scm (renpy): Likewise.
* gnu/packages/games.scm (roguebox-adventures)
(seahorse-adventures, kajongg): Likewise.
* gnu/packages/gimp.scm (gimp, glimpse): Likewise.
* gnu/packages/glib.scm (itstool): Likewise.
* gnu/packages/gnome.scm (gnome-music, gtg, rhythmbox): Likewise.
(eolie, d-feet, gedit, caribou, gnome-shell, authenticator)
(gnome-todo, orca, passwordsafe, terminator, setzer)
(libratbag, komikku): Likewise.
* gnu/packages/gps.scm (gpsd): Likewise.
* gnu/packages/gtk.scm (gtk-doc): Likewise.
* gnu/packages/ibus.scm (ibus, ibus-libpinyin, ibus-anthy)
(ibus-libhangul): Likewise.
* gnu/packages/inkscape.scm (inkscape-1.0): Likewise.
* gnu/packages/linux.scm (bcc): Likewise.
* gnu/packages/mail.scm (notifymuch): Likewise.
* gnu/packages/maths.scm (units): Likewise.
* gnu/packages/music.scm (solfege): Likewise.
* gnu/packages/networking.scm (blueman): Likewise.
* gnu/packages/patchutils.scm (patchwork): Likewise.
* gnu/packages/photo.scm (rapid-photo-downloader, entangle): Likewise.
* gnu/packages/plotutils.scm (asymptote): Likewise.
* gnu/packages/presentation.scm (presentty): Likewise.
* gnu/packages/screen.scm (byobu): Likewise.
* gnu/packages/storage.scm (ceph): Likewise.
* gnu/packages/syndication.scm (liferea): Likewise.
* gnu/packages/task-management.scm (blanket): Likewise.
* gnu/packages/text-editors.scm (manuskript): Likewise.
* gnu/packages/version-control.scm (gitless, cgit, git-when-merged)
(git-imerge): Likewise.
* gnu/packages/video.scm (pitivi): Likewise.
* gnu/packages/virtualization.scm (criu): Likewise.
* gnu/packages/xfce.scm (catfish): Likewise.
2021-02-01 11:54:01 -05:00
44db90b39f
gnu: python-loompy: Do not set PYTHONPATH.
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* gnu/packages/bioinformatics.scm (python-loompy)
[phases]{check}: Do not set PYTHONPATH.
2021-02-01 11:53:47 -05:00
21ce20bd2f
gnu: python-scanpy: Do not set PYTHONPATH.
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* gnu/packages/bioinformatics.scm (python-scanpy)[phases]
{check}: Do not set PYTHONPATH.
2021-02-01 11:53:47 -05:00
3c0b373310
gnu: python-screed: Adjust following Python build system changes.
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* gnu/packages/bioinformatics.scm (python-screed)[arguments]: Remove field, no
longer necessary.
2021-02-01 11:53:47 -05:00
5e47bebf3b
gnu: bamm: Update following changes to the Python build system.
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* gnu/packages/bioinformatics.scm (bamm): Delete trailing #t.
[phases]{check}: Override rather than delete phase. Remove trailing #t.
{post-install-check}: Delete phase.
{wrap-executable}: Also wrap with the new GUIX_PYTHONPATH.
2021-02-01 11:53:46 -05:00
98769a7709
gnu: python-pysam: Adjust following Python build system changes.
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* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Remove the
'#:modules' argument.
[phases]: Remove trailing #t.
{check}: Do not manually set PYTHONPATH.
2021-02-01 11:53:46 -05:00
25798ca0e0
gnu: python-pybedtools: Streamline following Python build system changes.
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* gnu/packages/bioinformatics.scm (python-pybedtools): Remove trailing #t.
[phases]{check}: Do not manually set PYTHONPATH.
[arguments]: Remove the '#:modules' argument.
2021-02-01 11:53:46 -05:00
82f5f6b14c
gnu: Replace all uses of texlive-union by texlive-updmap.cfg.
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* doc/build.scm (pdf-manual) Replace texlive-union by texlive-updmap.cfg.
* gnu/packages/algebra.scm (pari-gp): Likewise.
* gnu/packages/bioinformatics.scm (discrover, velvet): Likewise.
* gnu/packages/chez.scm (chez-scheme, chez-web, chez-sockets): Likewise.
* gnu/packages/docbook.scm (dblatex): Likewise.
* gnu/packages/emacs-xyz.scm (emacs-auctex): Likewise.
* gnu/packages/engineering.scm (fastcap): Likewise.
* gnu/packages/guile-xyz.scm (emacsy, guile-cv): Likewise.
* gnu/packages/lisp.scm (sbcl): Likewise.
* gnu/packages/maths.scm (octave, hypre): Likewise.
* gnu/packages/music.scm (lilypond): Likewise.
* gnu/packages/plotutils.scm (asymptote): Likewise.
* gnu/packages/python-xyz.scm (python-numpy-documentation)
(python-matplotlib-documentation, python-ipython-documentation)
(python-pypandoc): Likewise.
* gnu/packages/radio.scm (gnuradio, libosmo-dsp): Likewise.
* gnu/packages/scheme.scm (mit-scheme): Likewise.
* gnu/packages/statistics.scm (r-with-tests): Likewise.
* gnu/packages/tex.scm (simple-texlive-package)
(texlive-xmltex, texlive-tiny, texlive-jadetex, teximpatient, lyx): Likewise.
2021-01-29 13:35:47 -05:00
23a5dcce1d
gnu: grocsvs: Remove package.
...
This package depends on Python 2 and doesn't build anymore. Upstream doesn't
seem active, but if they ever port it to Python 3, they should let people know
here: https://github.com/grocsvs/grocsvs/issues/6 .
* gnu/packages/bioinformatics.scm (grocsvs): Delete.
2021-01-29 10:58:25 -05:00
c4a2cbeb06
gnu: Add r-demultiplex.
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* gnu/packages/bioinformatics.scm (r-demultiplex): New variable.
2021-01-28 22:24:51 +01:00
04b1a1f6bd
gnu: Add repeat-masker.
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* gnu/packages/bioinformatics.scm (repeat-masker): New variable.
2021-01-28 15:07:55 +01:00
6d3cafa086
gnu: Add trf.
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* gnu/packages/bioinformatics.scm (trf): New variable.
2021-01-28 15:07:55 +01:00
b3e39a475f
gnu: freebayes: Update source, home-page URIs.
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* gnu/packages/bioinformatics.scm (freebayes)[source]: Update to new
upstream URI.
[home-page]: Same.
2021-01-19 11:48:38 +02:00
99043adf46
gnu: freebayes: Don't include vcflib sources.
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* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Remove
vcflib-source, intervaltree-source. Move vcflib ...
[inputs]: ... to here.
[arguments]: Adjust 'patch-source and 'unpack-submodule-sources for
changes in vendored code.
* gnu/packages/patches/freebayes-devendor-deps.patch: Update patch.
2021-01-19 11:41:07 +02:00
1bbfe1789d
gnu: vcflib: Add pkg-config file.
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* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
create pkg-config file.
2021-01-19 11:36:01 +02:00
d6a8148c8d
gnu: vcflib: Build a shared library.
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* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
build a shared library instead of a static one.
2021-01-19 10:43:06 +02:00
797585746b
gnu: freebayes: Extend test timeout on slower architectures.
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* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Use custom
'check phase on aarch64-linux and armhf-linux to extend the test timeout.
2021-01-19 10:33:19 +02:00
c0afd8044f
gnu: Add r-snapatac.
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* gnu/packages/bioinformatics.scm (r-snapatac): New variable.
2021-01-18 23:26:53 +01:00
2d9c6542c8
gnu: mafft: Update to 7.475.
...
* gnu/packages/bioinformatics.scm (mafft): Update to 7.475.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-01-18 11:57:28 +02:00
6cb86e23a9
gnu: ruby-bio-vcf: Rename to bio-vcf.
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This package is widely known in select circles specifically as 'bio-vcf'.
* gnu/packages/bioinformatics.scm (ruby-bio-vcf): Rename to bio-vcf.
2021-01-18 11:19:37 +02:00
9b6cddd32d
gnu: Add ruby-bio-vcf.
...
* gnu/packages/bioinformatics.scm (ruby-bio-vcf): New variable.
2021-01-18 10:41:46 +02:00
fc9fd5496f
gnu: freebayes: Update to 1.3.3.
...
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.3.
[source]: Add patch. Add snippet to remove vendored library.
[build-system]: Switch to meson-build-system.
[inputs]: Remove bamtools. Add fastahack, smithwaterman, tabixpp.
[native-inputs]: Remove procps, python-2, tabixpp source, smithwaterman
source, multichoose source, fsom source, filevercmp source, fastahack
source, bash-tap source. Add bash-tap, grep, pkg-config, simde, vcflib.
[arguments]: Drop make-flags. Don't delete 'configure phase. Delete
custom 'fix-tests, 'build-tabixpp-and-vcflib, 'fix-makefiles, 'install
phases. Adjust 'unpack-submodule-sources phase to changed native-inputs.
Add new 'patch-source phase.
2021-01-17 15:47:32 +02:00
3ddeefe854
gnu: multichoose: Install header files.
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* gnu/packages/bioinformatics.scm (multichoose)[arguments]: Adjust
'install phase to also install header files.
2021-01-17 15:47:32 +02:00
976603b909
gnu: filevercmp: Install header files.
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* gnu/packages/bioinformatics.scm (filevercmp)[arguments]: Adjust
'install phase to install header files.
2021-01-17 15:47:32 +02:00
93309e25c7
gnu: vcflib: Update to 1.0.2.
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* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.2.
[source]: Download using git-fetch. Remove patch. Update snippet to use
packaged libraries.
[build-system]: Switch to cmake-build-system.
[inputs]: Add bzip2.
[native-inputs]: Add package-source of fsom.
[arguments]: Delete custom 'set-flags, 'install phases. Don't delete
'configure phase. Adjust 'unpack-submodule-sources phase.
* gnu/packages/patches/vcflib-use-shared-libraries.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2021-01-14 20:43:31 +02:00
db30d6eada
gnu: sambamba Update to 0.8.0.
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* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.0.
[source, home-page]: Update to new upstream URI.
[arguments]: Shorten 'fix-ldc-version phase. Remove
'place-biod-and-undead phase. Update 'unbundle-prerequisites and
'insatll phases.
[native-inputs]: Remove rdmd, biod. Move ldc ...
[inputs]: ... to here. Add zlib.
(htslib-for-sambamba): Remove variable.
2021-01-14 20:43:31 +02:00
2051be4f4c
gnu: gemma: Enable tests.
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* gnu/packages/bioinformatics.scm (gemma)[source]: Add snippet to remove
bundled sources.
[native-inputs]: Add catch-framework2-1, perl, shunit2, which.
[arguments]: Don't disable tests. Override 'check phase.
2021-01-14 20:43:31 +02:00
daf96e704d
gnu: gemma: Add Texinfo markup.
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* gnu/packages/bioinformatics.scm (gemma)[description]: Use Texinfo
markup.
2021-01-14 20:43:30 +02:00
a36abbe005
gnu: gemma: Update to 0.98.3.
...
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.3.
[source, home-page]: Update to new upstream URI.
[inputs]: Remove eigen, gfortran, lapack.
[arguments]: Remove make-flags. Remove 'find-eigen phase. Rename
'bin-mkdir phase to 'prepare-build and substitute openblas include
directory.
2021-01-14 20:43:30 +02:00
01f0707207
Merge branch 'staging' into 'core-updates'.
...
Conflicts:
gnu/local.mk
gnu/packages/cmake.scm
gnu/packages/curl.scm
gnu/packages/gl.scm
gnu/packages/glib.scm
gnu/packages/guile.scm
gnu/packages/node.scm
gnu/packages/openldap.scm
gnu/packages/package-management.scm
gnu/packages/python-xyz.scm
gnu/packages/python.scm
gnu/packages/tls.scm
gnu/packages/vpn.scm
gnu/packages/xorg.scm
2021-01-13 23:45:53 -05:00
610cd6a170
gnu: r-ggbio: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-ggbio): Move from here...
* gnu/packages/bioconductor.scm (r-ggbio): ...to here.
2020-12-29 17:40:28 +01:00
81f481d6cd
gnu: r-gqtlstats: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
2020-12-29 17:40:28 +01:00
61ec8928c7
gnu: r-snpstats: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-snpstats): Move from here...
* gnu/packages/bioconductor.scm (r-snpstats): ...to here.
2020-12-29 17:40:28 +01:00
a2c66d18a5
gnu: r-homo-sapiens: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here...
* gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here.
Replace 'string-append' by 'bioconductor-uri' with 'annotation'.
2020-12-29 17:40:28 +01:00
8c2b7c9a2a
gnu: r-erma: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-erma): Move from here...
* gnu/packages/bioconductor.scm (r-erma): ...to here.
2020-12-29 17:40:28 +01:00
8f1237c350
gnu: r-ldblock: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-ldblock): Move from here...
* gnu/packages/bioconductor.scm (r-ldblock): ...to here.
2020-12-29 17:40:28 +01:00
9534e7b706
gnu: r-gqtlstats: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
2020-12-29 17:40:28 +01:00
2a4322f7c3
gnu: r-gviz: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gviz): Move from here...
* gnu/packages/bioconductor.scm (r-gviz): ...to here.
2020-12-29 17:40:28 +01:00
69a5e066c1
gnu: r-gwascat: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gwascat): Move from here...
* gnu/packages/bioconductor.scm (r-gwascat): ...to here.
2020-12-29 17:40:28 +01:00
838db0de5e
gnu: r-sushi: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-sushi): Move from here...
* gnu/packages/bioconductor.scm (r-sushi): ...to here.
2020-12-29 17:40:25 +01:00
07e08bc7d5
gnu: discrover: Use new texlive package names.
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* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
"texlive-fonts-cm" and "texlive-fonts-amsfonts" with their new names
"texlive-cm" and "texlive-amsfonts", respectively.
2020-12-23 10:10:58 +01:00
714d02b6b5
gnu: discrover: Remove obsolete build phase.
...
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove obsolete
build phase setenv-HOME.
2020-12-23 10:10:58 +01:00
6203b8e5bd
gnu: kentutils: Build with OpenSSL 1.1.
...
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL-1.0
to OPENSSL.
2020-12-20 16:30:42 +01:00
ca27b0e528
gnu: kentutils: Add a file name for the "samtabix" input.
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* gnu/packages/bioinformatics.scm (kentutils)[native-inputs]: For "samtabix",
add a file name on the origin.
2020-12-20 16:30:42 +01:00
48f77ecbb1
gnu: r-keggrest: Update to 1.30.1.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.1.
2020-12-09 23:30:12 +01:00
4745f0dfca
gnu: r-genomeinfodb: Update to 1.26.2.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.2.
2020-12-09 23:30:12 +01:00
baeaa02e75
gnu: r-biocstyle: Update to 2.18.1.
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* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.1.
2020-12-09 23:30:12 +01:00
4617cc7fd5
gnu: r-rhtslib: Propagate zlib.
...
* gnu/packages/bioinformatics.scm (r-rhtslib)[inputs]: Move zlib from here...
[propagated-inputs]: ...to here.
(r-variantannotation, r-rsamtools, r-bamsignals, r-rhdf5,
r-methylkit)[inputs]: Remove zlib.
* gnu/packages/bioconductor.scm (r-diffbind, r-quasr, r-cytolib, r-ncdfflow,
r-flowworkspace, r-seqbias)[inputs]: Remove zlib.
2020-12-09 12:12:48 +01:00
Christopher Baines
Efraim Flashner
Maxim Cournoyer
Ricardo Wurmus
Mădălin Ionel Patrașcu
zimoun
Marius Bakke