b15e543d30
Merge branch 'master' into core-updates-frozen
2021-11-23 11:29:38 +01:00
e74bcbc64f
gnu: python-scanpy: Set PYTHONPATH variable.
...
This is a follow-up to commit 664721422c
2021-11-21 09:07:50 +01:00
6c9bbf8071
gnu: python-scanpy: Update to 1.8.2.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.2.
[arguments]: Disable test_clustermap test.
2021-11-21 09:07:50 +01:00
1a9665743b
gnu: perl-cworld-dekker: Use GUIX_PYTHONPATH.
...
* gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use
GUIX_PYTHONPATH.
2021-11-21 00:40:34 +01:00
664721422c
gnu: python-scanpy: Use GUIX_PYTHONPATH.
...
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Use
GUIX_PYTHONPATH instead of PYTHONPATH.
2021-11-21 00:39:57 +01:00
55870e86d9
gnu: multiqc: Remove sanity check.
...
* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Delete 'sanity-check phase.
2021-11-21 00:39:09 +01:00
e2ca652c98
gnu: multiqc: Use GUIX_PYTHONPATH.
...
* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Replace PYTHONPATH
with GUIX_PYTHONPATH.
2021-11-21 00:39:05 +01:00
c618f4a9cc
gnu: pigx-bsseq: Update to 0.1.6.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.6.
2021-11-20 16:31:32 +01:00
a8eea7a51e
gnu: qtltools: Fix typo.
...
* gnu/packages/bioinformatics.scm (qtltools)[description]: Switch from "allows
to go" to "allows going".
2021-11-18 14:20:07 -08:00
dddc90a363
gnu: shorah: Use GUIX_PYTHONPATH in wrapper.
...
* gnu/packages/bioinformatics.scm (shorah)[arguments]: Wrap executable with
GUIX_PYTHONPATH.
2021-11-18 19:25:16 +00:00
3a317f7476
Merge branch 'master' into core-updates-frozen
2021-11-17 23:43:14 +01:00
0a9a00b34c
gnu: pplacer: Fix build.
...
* gnu/packages/bioinformatics.scm (pplacer): Add missing input.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-11-16 15:43:51 +02:00
616bcc9c0b
gnu: python-scanpy: Run tests conditionally.
...
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Respect TESTS?
argument.
2021-11-15 15:21:06 +00:00
a0fc9e38fa
gnu: ciri-long: Move Cython to native inputs.
...
* gnu/packages/bioinformatics.scm (ciri-long)[inputs]: Move python-cython from
here...
[native-inputs]: ...to here.
2021-11-11 15:39:19 +00:00
c4e5fabb6e
gnu: ciri-long: Fix reference to ccs.
...
* gnu/packages/bioinformatics.scm (ciri-long)[arguments]: Add build phase
"fix-reference-to-ccs".
[inputs]: Add circtools.
2021-11-11 15:39:19 +00:00
6be47c5bc5
gnu: Add circtools.
...
* gnu/packages/bioinformatics.scm (circtools): New variable.
2021-11-11 15:39:19 +00:00
b8c9f061e1
gnu: Add bioparser.
...
* gnu/packages/bioinformatics.scm (bioparser): New variable.
2021-11-11 15:39:19 +00:00
4052310e91
gnu: Add biosoup.
...
* gnu/packages/bioinformatics.scm (biosoup): New variable.
2021-11-11 15:39:19 +00:00
1c94392a13
Merge remote-tracking branch 'origin/master' into core-updates-frozen
2021-11-08 09:06:14 +02:00
d54a4285ea
gnu: bedtools-2.18: Fix build with newer toolchain.
...
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Add phase
'compatibility, fixing syntax quirks that are problematic with newer
toolchains.
[native-inputs]: Do not inherit.
[inherit]: Do not inherit.
2021-11-03 21:07:29 +00:00
bc5155b952
Merge remote-tracking branch 'origin/master' into core-updates-frozen
2021-10-31 14:49:47 +02:00
41e5c12c4a
gnu: sailfish: Use TBB 2020.
...
* gnu/packages/bioinformatics.scm (sailfish)[inputs]: Replace tbb with
tbb-2020.
2021-10-24 21:38:25 +00:00
1bf55a4850
gnu: sailfish: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Remove trailing #T in
build phases...
[inputs]: ...and in the origin snippet of "rapmap".
2021-10-24 21:37:39 +00:00
4392783232
gnu: sailfish: Do not attempt to unpack a directory.
...
patch-and-repack no longer outputs a compressed archive when the input was a
directory.
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Adjust build phase
'prepare-rapmap.
2021-10-24 21:35:57 +00:00
57c233b37b
gnu: jellyfish: Remove Ruby bindings.
...
These bindings no longer build and we have no package that would need them.
* gnu/packages/bioinformatics.scm (jellyfish)[outputs]: Remove "ruby" output.
[arguments]: Remove option for building Ruby bindings.
[native-inputs]: Remove ruby.
2021-10-24 21:34:26 +00:00
da526f33f2
gnu: cutadapt: Regenerate Cython files.
...
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Add phase
'always-cythonize.
2021-10-24 21:23:20 +00:00
4faca03bed
gnu: python-dnaio: Update to 0.6.0.
...
* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.6.0.
2021-10-24 19:47:20 +00:00
238f47c76f
gnu: macs: Fix build by setting HOME.
...
* gnu/packages/bioinformatics.scm (macs)[arguments]: Add build phase to set
HOME variable.
2021-10-24 19:09:35 +00:00
1d01043a4f
gnu: methyldackel: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove trailing #T
from build phase.
2021-10-24 19:01:22 +00:00
2820b03509
gnu: methyldackel: Pass -fcommon to compiler.
...
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Add -fcommon to
CFLAGS.
2021-10-24 19:00:53 +00:00
cc331ad7eb
gnu: flexbar: Use TBB 2020.
...
* gnu/packages/bioinformatics.scm (flexbar)[inputs]: Replace tbb with
tbb-2020.
2021-10-24 18:50:09 +00:00
084bdf9d69
gnu: flexbar: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Remove trailing #T
from all build phases.
2021-10-24 18:49:43 +00:00
d0a1d798ee
gnu: bwa: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove trailing #T in
build phase.
2021-10-24 18:48:53 +00:00
2da99b671e
gnu: bwa: Pass -fcommon to compiler.
...
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Add -fcommon option to
CFLAGS.
2021-10-24 18:48:20 +00:00
724972bcca
gnu: bowtie1: Use TBB 2020.
...
* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Replace tbb with
tbb-2020.
2021-10-24 18:47:45 +00:00
f336cc4fe7
gnu: bowtie: Replace invalid characters.
...
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace invalid quotes
with straight quotes in the 'configure phase.
2021-10-24 18:44:57 +00:00
e5a26a1f02
gnu: bowtie: Remove trailing #T.
...
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Remove trailing #T from
build phases...
[source]: ...and from the snippet.
2021-10-24 16:59:39 +00:00
2ec601580b
gnu: bowtie: Use TBB 2020.
...
* gnu/packages/bioinformatics.scm (bowtie)[inputs]: Replace tbb with tbb-2020.
2021-10-24 16:58:58 +00:00
973b21aa6a
gnu: Add r-umi4cpackage.
...
* gnu/packages/bioinformatics.scm (r-umi4cpackage): New variable.
2021-10-24 13:45:46 +00:00
42873c2b06
gnu: tbb-for-salmon: Rename.
...
* gnu/packages/tbb.scm (tbb-for-salmon): Rename this variable...
(tbb-2020): ...to this.
* gnu/packages/bioinformatics.scm (salmon)[inputs]: Rename it.
2021-10-24 13:28:05 +00:00
4a0cd6297a
gnu: Add qtltools.
...
* gnu/packages/bioinformatics.scm (qtltools): New variable.
2021-10-22 21:29:25 +00:00
a8bac123f0
gnu: Add gdc-client.
...
* gnu/packages/bioinformatics.scm (gdc-client): New variable.
2021-10-21 14:49:01 +00:00
f65917f607
gnu: Add r-shaman.
...
* gnu/packages/bioinformatics.scm (r-shaman): New variable.
2021-10-21 14:34:35 +00:00
4885f40b80
gnu: Add r-misha.
...
* gnu/packages/bioinformatics.scm (r-misha): New variable.
2021-10-21 14:25:44 +00:00
42c9b75b25
gnu: Add ciri-long.
...
* gnu/packages/bioinformatics.scm (ciri-long): New variable.
2021-10-21 13:39:36 +00:00
10664fcc8c
gnu: python-biopython: Update to 1.76.
...
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.76.
(python-biopython-1.73): New variable.
(instrain)[inputs]: Replace python-biopython with python-biopython-1.73.
2021-10-21 13:33:51 +00:00
36cf0253a9
gnu: instrain: Update to 1.5.4.
...
* gnu/packages/bioinformatics.scm (instrain): Update to 1.5.4.
2021-10-21 13:32:37 +00:00
57841a91f5
gnu: Add python-bwapy.
...
* gnu/packages/bioinformatics.scm (python-bwapy): New variable.
2021-10-21 12:23:25 +00:00
6526c35df5
gnu: Add python-pyspoa.
...
* gnu/packages/bioinformatics.scm (python-pyspoa): New variable.
2021-10-21 12:23:22 +00:00
174c29a8e0
gnu: salmon: Use older version of TBB.
...
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Define
HAVE_NUMERIC_LIMITS128; compute TBB_VERSION.
[inputs]: Replace tbb with tbb-for-salmon.
2021-10-19 06:28:30 +00:00
a1eca979fb
Merge remote-tracking branch 'origin/master' into core-updates-frozen.
2021-10-12 17:46:23 +00:00
9101c7bf8e
gnu: clipper: Disable non-deterministic test.
...
This test fails/succeeds non-deterministically.
* gnu/packages/bioinformatics.scm (clipper)[arguments]: Disable
non-deterministic test test_get_FDR_cutoff_mean.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-10-12 18:13:29 +02:00
c8a7ba621b
gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc.
...
* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
2021-10-08 09:13:55 +02:00
26488f63b8
gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc.
...
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
2021-10-08 09:13:55 +02:00
07f2e4993b
gnu: pigx-chipseq: Remove dependency on pandoc-citeproc.
...
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
2021-10-08 09:13:54 +02:00
e51a3f4a72
gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc.
...
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[source]: Use it.
[native-inputs]: Add automake/autoconf.
2021-10-08 09:13:54 +02:00
fb1ffc53ba
gnu: pigx-bsseq: Remove dependency on pandoc-citeproc.
...
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
2021-10-08 09:13:54 +02:00
7eb9fe4e53
gnu: ngless: Fix build.
...
Apply upstream patch to restore compatibility with current Stackage.
* gnu/packages/patches/ngless-unliftio.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/bioinformatics.scm (ngless): Use it.
2021-10-08 09:13:53 +02:00
b97f549b14
gnu: Update Haskell ecosystem.
...
Bump packages’ versions to the lastest Stackage or Hackage
release. Since packages are interdependent, do so in a single commit.
525 packages have been updated.
These packages have been removed, because they fail to build, have no
newer version available and no dependencies:
corrode
ghc-easytest
ghc-edisonapi
ghc-edisoncore
ghc-pandoc-types
ghc-regex-tdfa-text
These have been removed, because they are no longer required:
ghc-happy-1.19.9
ghc-prettyprinter-1.6
ghc-protolude-0.3
ghc-pandoc-citeproc and pandoc-citeproc have been removed, because pandoc
does not use them any more.
Co-authored-by: Xinglu Chen <public@yoctocell.xyz>
2021-10-08 09:13:52 +02:00
53611ab5c5
gnu: pigx-chipseq: Update to 0.0.53.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.53.
[inputs]: Add r-hexbin.
2021-09-29 09:58:45 +02:00
f36b789f78
gnu: Update some packages using old JavaScript minifier.
...
* gnu/packages/minetest.scm (minetest-basic-trains): New variable.
* gnu/packages/bioinformatics.scm (bismark): Update uglifyjs input.
* gnu/packages/ci.scm (laminar): Update uglifyjs input.
* gnu/packages/cran.scm (r-shiny r-shinytree r-shinydashboard r-colourpicker
r-threejs r-flexdashboard r-networkd3 r-dygraphs): Update uglifyjs input.
* gnu/packages/javascript.scm (js-mathjax): Update uglifyjs input.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-09-22 16:03:19 +03:00
f80824fe09
gnu: Add r-presto.
...
* gnu/packages/bioinformatics.scm (r-presto): New variable.
2021-09-20 17:23:16 +02:00
0406f1c2e1
gnu: discrover: Update package name in texlive-union.
...
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
texlive-fonts-cm with texlive-cm.
2021-09-13 22:49:56 +02:00
d9dfbf886d
Merge branch 'master' into core-updates-frozen
2021-09-07 14:19:08 +02:00
b949f34f31
gnu: Use the non-deprecated TeX packages.
...
This commit leaves 'dblatex' and 'texlive-hyperref' as users of
deprecated packages, but these have many dependents.
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use
non-deprecated TeX Live packages.
(velvet)[native-inputs]: Likewise.
* gnu/packages/chez.scm (chez-scheme)[native-inputs]: Likewise.
(chez-web)[native-inputs]: Likewise.
* gnu/packages/engineering.scm (fastcap)[native-inputs]: Likewise.
* gnu/packages/guile-xyz.scm (emacsy)[native-inputs]: Likewise.
* gnu/packages/maths.scm (hypre)[native-inputs]: Likewise.
* gnu/packages/music.scm (lilypond)[native-inputs]: Likewise.
* gnu/packages/ocaml.scm (ocaml-bibtex2html)[native-inputs]: Likewise.
* gnu/packages/plotutils.scm (asymptote)[native-inputs]: Likewise.
* gnu/packages/python-xyz.scm (python-numpy-documentation)[native-inputs]:
Likewise.
(python-matplotlib-documentation)[native-inputs]: Likewise.
(python-ipython-documentation)[native-inputs]: Likewise.
(python-nbconvert)[native-inputs]: Likewise.
(python-pypandoc)[native-inputs]: Likewise.
* gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Likewise.
* gnu/packages/tex.scm (texlive-pstool)[propagated-inputs]: Likewise.
(teximpatient)[native-inputs]: Likewise.
(texlive-latex-pgf)[propagated-inputs]: Likewise.
(texlive-beamer)[propagated-inputs]: Likewise.
2021-09-06 22:02:15 +02:00
c82b723bf8
gnu: Add megadepth.
...
* gnu/packages/bioinformatics.scm (megadepth): New variable.
2021-09-06 14:48:24 +02:00
93bf42361c
gnu: Replace PYTHONPATH with GUIX_PYTHONPATH.
...
In packages that do not use python-build-system, PYTHONPATH is generally
not defined. Instead we can use GUIX_PYTHONPATH which should contain all
Python dependencies.
* gnu/packages/bioinformatics.scm (shorah)[arguments]: Replace
PYTHONPATH with GUIX_PYTHONPATH.
* gnu/packages/debug.scm (c-vise)[arguments]: Idem.
* gnu/packages/gnome.scm (drawing, apostrophe, ocrfeeder)[arguments]: Idem.
* gnu/packages/music.scm (a2jmidid)[arguments]: Idem.
* gnu/packages/syndication.scm (gfeeds)[arguments]: Idem.
* gnu/packages/xdisorg.scm (gammastep)[arguments]: Idem.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
2021-09-06 10:47:54 +02:00
c75b30d58f
gnu: Add r-catch.
...
* gnu/packages/bioinformatics.scm (r-catch): New variable.
2021-09-01 14:53:36 +02:00
4abf226833
gnu: Add scregseg.
...
* gnu/packages/bioinformatics.scm (scregseg): New variable.
2021-08-31 23:11:06 +02:00
a1ee212184
gnu: python-strawc: Propagate pybind11.
...
* gnu/packages/bioinformatics.scm (python-strawc)[inputs]: Move pybind11 from
here...
[propagated-inputs]: ...to here.
2021-08-31 23:11:05 +02:00
55cb5a62a1
gnu: python-scanpy: Propagate sinfo.
...
* gnu/packages/bioinformatics.scm (python-scanpy)[native-inputs]: Move
python-sinfo from here...
[propagated-inputs]: ...to here.
2021-08-31 23:11:05 +02:00
c4133c43c7
Merge branch 'master' into core-updates-frozen
...
Conflicts:
gnu/packages/algebra.scm
gnu/packages/games.scm
gnu/packages/golang.scm
gnu/packages/kerberos.scm
gnu/packages/mail.scm
gnu/packages/python.scm
gnu/packages/ruby.scm
gnu/packages/scheme.scm
gnu/packages/tex.scm
gnu/packages/tls.scm
gnu/packages/version-control.scm
2021-08-12 00:30:27 +02:00
b029be2ee0
Merge branch 'master' into core-updates-frozen
...
Conflicts:
gnu/packages/bioinformatics.scm
gnu/packages/cmake.scm
gnu/packages/curl.scm
gnu/packages/emacs-xyz.scm
gnu/packages/gpodder.scm
gnu/packages/music.scm
gnu/packages/patches/glibc-bootstrap-system.patch
gnu/packages/python-xyz.scm
gnu/packages/shells.scm
gnu/packages/statistics.scm
2021-07-29 22:34:57 +02:00
7712154ccb
gnu: Add python-coolbox.
...
* gnu/packages/bioinformatics.scm (python-coolbox): New variable.
2021-08-30 18:29:57 +02:00
b105655670
gnu: python-scanpy: Update to 1.8.1.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.8.1.
[arguments]: Bulid with flit; update list of broken tests.
[native-inputs]: Add python-flit and python-anndata:source.
2021-08-30 18:29:57 +02:00
d84ead8174
gnu: Add python-dna-features-viewer.
...
* gnu/packages/bioinformatics.scm (python-dna-features-viewer): New variable.
2021-08-30 18:29:56 +02:00
e85b35070c
gnu: Add python-pybbi.
...
* gnu/packages/bioinformatics.scm (python-pybbi): New variable.
2021-08-30 18:29:56 +02:00
db13eb962f
gnu: Add python-strawc.
...
* gnu/packages/bioinformatics.scm (python-strawc): New variable.
2021-08-27 13:37:29 +02:00
17c765e2e1
gnu: Add r-cytonorm.
...
* gnu/packages/bioinformatics.scm (r-cytonorm): New variable.
2021-08-27 13:37:29 +02:00
f66759e0b2
gnu: Add ivar.
...
* gnu/packages/bioinformatics.scm (ivar): New variable.
2021-08-25 11:22:02 +02:00
27952318a5
gnu: fastp: Update to 0.20.1.
...
* gnu/packages/bioinformatics.scm (fastp): Update to 0.20.1.
[arguments]: Set PREFIX instead of BINDIR.
2021-08-20 10:49:48 +02:00
907f835e19
gnu: pigx-rnaseq: Update to 0.0.18.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.18.
2021-08-11 19:33:38 +02:00
a79ad5fce5
gnu: pigx-rnaseq: Update to 0.0.19.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.19.
2021-08-13 15:23:39 +02:00
f1b64c435a
gnu: pigx-sars-cov2-ww: Update to 0.0.3.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.3.
2021-08-05 16:46:34 +02:00
2ab5d08fbe
gnu: Add r-spectre.
...
* gnu/packages/bioinformatics.scm (r-spectre): New variable.
2021-08-03 10:43:08 +02:00
3e5eff8c30
gnu: Add seqan 3.
...
* gnu/packages/bioinformatics.scm (seqan): Rename this variable...
(seqan-2): ...to this.
(seqan): New variable for seqan3.
(flexbar)[native-inputs]: Update name for seqan 2.
2021-07-26 11:54:21 +02:00
99ca1ae4f8
gnu: Add segemehl.
...
* gnu/packages/bioinformatics.scm (segemehl): New variable.
2021-07-26 11:08:13 +02:00
d468a03a00
gnu: Use 'search-input-directory' and 'search-input-file' where appropriate.
...
This changes some of the remaining uses of this idiom:
(string-append (assoc-ref inputs "LABEL") "FILE")
to one of:
(search-input-file inputs "FILE")
(search-input-directory inputs "FILE")
* gnu/packages/axoloti.scm (axoloti-patcher): Use
'search-input-directory'.
(axoloti-patcher-next): Likewise.
* gnu/packages/bioinformatics.scm (java-picard): Likewise.
* gnu/packages/bootloaders.scm (grub-hybrid): Likewise.
(u-boot-puma-rk3399): Likewise.
(u-boot-rock64-rk3328): Likewise.
(u-boot-firefly-rk3399): Likewise.
(u-boot-rockpro64-rk3399): Likewise.
(u-boot-pinebook-pro-rk3399): Likewise.
* gnu/packages/cran.scm (r-shiny): Likewise.
(r-shinytree): Likewise.
* gnu/packages/education.scm (anki): Likewise.
* gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte): Likewise.
(emacs-rime): Likewise.
* gnu/packages/emulators.scm (dolphin-emu): Likewise.
* gnu/packages/games.scm (bsd-games): Likewise.
(seahorse-adventures): Likewise.
(einstein): Likewise.
* gnu/packages/gimp.scm (gimp-fourier): Likewise.
* gnu/packages/gnome.scm (gspell): Likewise.
* gnu/packages/guile-xyz.scm (guile-libyaml): Likewise.
* gnu/packages/java.scm (icedtea-7): Likewise.
* gnu/packages/language.scm (nimf): Likewise.
* gnu/packages/lxde.scm (spacefm): Likewise.
* gnu/packages/mail.scm (claws-mail): Likewise.
* gnu/packages/netpbm.scm (netpbm): Likewise.
* gnu/packages/networking.scm (blueman): Likewise.
* gnu/packages/scheme.scm (scm): Likewise.
* gnu/packages/security-token.scm (python-fido2): Likewise.
* gnu/packages/syndication.scm (rtv): Likewise.
* gnu/packages/tls.scm (acme-client): Likewise.
* gnu/packages/web.scm (netsurf): Likewise.
* gnu/packages/wine.scm (wine-staging): Likewise.
* gnu/packages/wxwidgets.scm (wxwidgets): Likewise.
2021-07-24 16:23:24 +02:00
828cfdc47e
gnu: Use 'search-input-file' when looking for .jar files.
...
* gnu/packages/bioinformatics.scm (java-picard-1.113): Use
'search-input-file' when looking for *.jar.
(fastqc): Likewise.
* gnu/packages/groovy.scm (groovy): Likewise.
* gnu/packages/java.scm (ant-bootstrap): Likewise.
(ecj-bootstrap): Likewise.
(java-cisd-base): Likewise.
(java-cisd-args4j): Likewise.
(java-cisd-jhdf5): Likewise.
(java-native-access): Likewise.
(java-native-access-platform): Likewise.
* gnu/packages/maths.scm (hdf-java): Likewise.
2021-07-24 16:23:23 +02:00
bc64d9554b
gnu: Use 'search-input-file' when looking for executables.
...
* gnu/packages/admin.scm (isc-dhcp): Use 'search-input-file' when
looking for executables.
* gnu/packages/audio.scm (ableton-link): Likewise.
* gnu/packages/benchmark.scm (fio): Likewise.
* gnu/packages/bioinformatics.scm (roary): Likewise.
(ngless): Likewise.
* gnu/packages/boost.scm (boost-for-irods): Likewise.
* gnu/packages/bootloaders.scm (grub): Likewise.
(grub-efi): Likewise.
* gnu/packages/chemistry.scm (inchi): Likewise.
* gnu/packages/dictionaries.scm (ding): Likewise.
* gnu/packages/dlang.scm (ldc): Likewise.
* gnu/packages/education.scm (childsplay): Likewise.
* gnu/packages/emacs-xyz.scm (emacs-hyperbole): Likewise.
(emacs-haskell-mode): Likewise.
(emacs-auctex): Likewise.
(emacs-ggtags): Likewise.
(emacs-graphviz-dot-mode): Likewise.
(emacs-flycheck-grammalecte): Likewise.
(emacs-counsel-notmuch): Likewise.
(emacspeak): Likewise.
(emacs-exwm): Likewise.
(emacs-exwm-x): Likewise.
(emacs-treemacs): Likewise.
(emacs-telega): Likewise.
(emacs-exiftool): Likewise.
* gnu/packages/emulators.scm (higan): Likewise.
* gnu/packages/engineering.scm (freehdl): Likewise.
(librepcb): Likewise.
* gnu/packages/entr.scm (entr): Likewise.
* gnu/packages/file-systems.scm (libeatmydata): Likewise.
(xfstests): Likewise.
(mergerfs): Likewise.
(mergerfs-tools): Likewise.
* gnu/packages/finance.scm (monero-gui): Likewise.
* gnu/packages/flashing-tools.scm (flashrom): Likewise.
* gnu/packages/fontutils.scm (fontforge): Likewise.
* gnu/packages/game-development.scm (python2-renpy): Likewise.
* gnu/packages/games.scm (opensurge): Likewise.
(xboard): Likewise.
(hyperrogue): Likewise.
(flare-game): Likewise.
(chessx): Likewise.
* gnu/packages/geo.scm (grass): Likewise.
* gnu/packages/glib.scm (glib): Likewise.
* gnu/packages/gnome.scm (mm-common): Likewise.
(network-manager-openvpn): Likewise.
(network-manager-vpnc): Likewise.
(network-manager-openconnect): Likewise.
(apostrophe): Likewise.
* gnu/packages/gnupg.scm (pius): Likewise.
(jetring): Likewise.
* gnu/packages/gnuzilla.scm (icedove): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
* gnu/packages/graphviz.scm (xdot): Likewise.
* gnu/packages/guile-xyz.scm (jupyter-guile-kernel): Likewise.
* gnu/packages/haskell-xyz.scm (ghc-hindent): Likewise.
* gnu/packages/ibus.scm (ibus): Likewise.
* gnu/packages/image.scm (phockup): Likewise.
* gnu/packages/irc.scm (quassel): Likewise.
* gnu/packages/java.scm (drip): Likewise.
(ant-bootstrap): Likewise.
(tla2tools): Likewise.
* gnu/packages/julia.scm (julia): Likewise.
* gnu/packages/less.scm (lesspipe): Likewise.
* gnu/packages/libreoffice.scm (libreoffice): Likewise.
* gnu/packages/linux.scm (fuse): Likewise.
(lm-sensors): Likewise.
(bluez): Likewise.
(fakeroot): Likewise.
(inputattach): Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-cl-diskspace): Likewise.
* gnu/packages/lisp.scm (lisp-repl-core-dumper): Likewise.
* gnu/packages/lua.scm (fennel): Likewise.
* gnu/packages/lxde.scm (spacefm): Likewise.
* gnu/packages/mail.scm (public-inbox): Likewise.
* gnu/packages/maths.scm (hdf-java): Likewise.
(maxima): Likewise.
(frama-c): Likewise.
* gnu/packages/messaging.scm (libgadu): Likewise.
* gnu/packages/music.scm (denemo): Likewise.
(curseradio): Likewise.
* gnu/packages/netpbm.scm (netpbm): Likewise.
* gnu/packages/networking.scm (blueman): Likewise.
(squid): Likewise.
(aircrack-ng): Likewise.
* gnu/packages/node.scm (node): Likewise.
(node-llparse-frontend-bootstrap): Likewise.
(node-llparse-bootstrap): Likewise.
(llhttp-bootstrap): Likewise.
(node-lts): Likewise.
* gnu/packages/ocaml.scm (ocaml-4.11): Likewise.
(opam): Likewise.
(ocaml-graph): Likewise.
* gnu/packages/orpheus.scm (orpheus): Likewise.
* gnu/packages/password-utils.scm (password-store): Likewise.
* gnu/packages/python.scm (pypy3): Likewise.
* gnu/packages/qt.scm (qt5ct): Likewise.
* gnu/packages/radio.scm (libosmo-dsp): Likewise.
* gnu/packages/ruby.scm (ruby-pandoc-ruby): Likewise.
* gnu/packages/rust.scm (rust-1.30): Likewise.
* gnu/packages/screen.scm (byobu): Likewise.
* gnu/packages/statistics.scm (r-with-tests): Likewise.
* gnu/packages/suckless.scm (surf): Likewise.
* gnu/packages/syndication.scm (gfeeds): Likewise.
* gnu/packages/telephony.scm (mumble): Likewise.
* gnu/packages/terminals.scm (alacritty): Likewise.
* gnu/packages/tex.scm (texlive-bin): Likewise.
* gnu/packages/uml.scm (plantuml): Likewise.
* gnu/packages/version-control.scm (python-git-multimail): Likewise.
(gitolite): Likewise.
(hg-commitsigs): Likewise.
(git-when-merged): Likewise.
(git-imerge): Likewise.
(gita): Likewise.
* gnu/packages/video.scm (you-get): Likewise.
* gnu/packages/vim.scm (eovim): Likewise.
* gnu/packages/virtualization.scm (qemu): Likewise.
(virt-manager): Likewise.
(criu): Likewise.
* gnu/packages/vpn.scm (strongswan): Likewise.
(xl2tpd): Likewise.
* gnu/packages/wm.scm (i3lock-fancy): Likewise.
* gnu/packages/wxwidgets.scm (python-wxpython): Likewise.
(python2-wxpython): Likewise.
* gnu/packages/xdisorg.scm (autorandr): Likewise.
* gnu/packages/xorg.scm (hackneyed-x11-cursors): Likewise.
(v86d): Likewise.
(mkfontdir): Likewise.
(xpra): Likewise.
2021-07-24 16:23:23 +02:00
377e9453ca
gnu: Use 'search-input-file' when looking for *.so and *.a.
...
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use
'search-input-file' when looking for *.a and *.so.
* gnu/packages/emulators.scm (dolphin-emu): Likewise.
* gnu/packages/engineering.scm (lepton-eda): Likewise.
(pcb): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
(go-1.14): Likewise.
* gnu/packages/haskell.scm (ghc-7): Likewise.
* gnu/packages/irods.scm (irods): Likewise.
* gnu/packages/language.scm (python2-tegaki-pygtk): Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-lzlib): Likewise.
(sbcl-cl-gobject-introspection): Likewise.
(sbcl-cl-ana): Likewise.
(sbcl-cl-libuv): Likewise.
(sbcl-cl-async): Likewise.
(sbcl-mcclim): Likewise.
(sbcl-zstd): Likewise.
(sbcl-cl-opengl): Likewise.
(sbcl-lev): Likewise.
(sbcl-cl-glfw3): Likewise.
* gnu/packages/machine-learning.scm (tensorflow): Likewise.
* gnu/packages/messaging.scm (utox): Likewise.
* gnu/packages/mpi.scm (java-openmpi): Likewise.
* gnu/packages/music.scm (jack-select): Likewise.
* gnu/packages/pascal.scm (fpc): Likewise.
* gnu/packages/python-crypto.scm (python-libnacl): Likewise.
* gnu/packages/python-xyz.scm (python-cairocffi): Likewise.
(python-pyev): Likewise.
(python-pytidylib): Likewise.
* gnu/packages/radio.scm (unixcw): Likewise.
* gnu/packages/rust.scm (rust-1.32): Likewise.
* gnu/packages/security-token.scm (opensc): Likewise.
(python-pyscard): Likewise.
* gnu/packages/selinux.scm (python-setools): Likewise.
* gnu/packages/spice.scm (libcacard): Likewise.
* gnu/packages/telephony.scm (libtgvoip): Likewise.
2021-07-24 16:23:23 +02:00
425ccde6ae
gnu: Use 'search-input-directory' when looking for C/C++ library headers.
...
* gnu/packages/arcan.scm (arcan)[arguments]: Use
'search-input-directory' for "include/libdrm" and "include/apr-1".
* gnu/packages/bioinformatics.scm (sailfish): Likewise for jellyfish.
* gnu/packages/boost.scm (boost-for-irods): Likewise for libcxx headers.
* gnu/packages/cedille.scm (cedille): Likewise for IAL headers.
* gnu/packages/compression.scm (snappy-with-clang6): Likewise for libcxx
headers.
* gnu/packages/cups.scm (hplip): Likewise for libusb headers.
* gnu/packages/emulators.scm (pcsxr): Likewise for libcdio headers.
* gnu/packages/game-development.scm (python2-renpy): Likewise for
fribidi headers.
* gnu/packages/games.scm (pokerth): Likewise for libircclient.
* gnu/packages/guile-xyz.scm (guile-persist): Likewise for Guile.
* gnu/packages/hurd.scm (hurd): Likewise for libtirpc.
* gnu/packages/irods.scm (irods, irods-client-icommands): Likewise for
libcxx, catch2, and nlohmann-json-cpp.
* gnu/packages/julia.scm (julia): Use 'search-input-file' for libuv's
errno.h.
* gnu/packages/kde-pim.scm (kdepim-runtime): Use
'search-input-directory' for "include/KF5".
(kmessagelib): Likewise.
* gnu/packages/kde.scm (kdeconnect): Likewise.
* gnu/packages/llvm.scm (clang-runtime-3.5): Likewise for libtirpc.
* gnu/packages/mpi.scm (openmpi): Likewise for "include/infiniband".
* gnu/packages/pumpio.scm (pumpa): Use 'search-input-file' for "tidy.h"
and "aspell.h".
* gnu/packages/radio.scm (dream): Use 'search-input-file' and
'search-input-directory' for pulseaudio, sndfile, etc.
* gnu/packages/selinux.scm (policycoreutils): Likewise for PAM and
libaudit.
* gnu/packages/serialization.scm (avro-cpp-1.9-for-irods): Likewise for
libcxx.
* gnu/packages/sync.scm (nextcloud-client): Likewise for "include/KF5".
* gnu/packages/video.scm (mkvtoolnix): Likewise for "include/gtest".
(libopenshot): Likewise for "include/UnitTest++".
* gnu/packages/virtualization.scm (criu): Likewise for libnl3 and for
protobuf file.
2021-07-24 16:23:23 +02:00
1ec13efbd2
gnu: Use 'search-input-directory' for the Eigen header directory.
...
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use
'search-input-directory' when searching for Eigen headers.
* gnu/packages/bioinformatics.scm (nanopolish): Likewise.
* gnu/packages/machine-learning.scm (tensorflow): Likewise.
2021-07-24 16:23:22 +02:00
6ea7297ea4
gnu: Use 'search-input-directory' when looking for tzdata.
...
* gnu/packages/backup.scm (duplicity)[arguments]: Use
'search-input-directory' for "share/zoneinfo".
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Likewise.
(pigx-bsseq): Likewise.
* gnu/packages/calcurse.scm (calcurse): Likewise.
* gnu/packages/calendar.scm (date): Likewise.
* gnu/packages/compression.scm (lhasa): Likewise.
* gnu/packages/cran.scm (r-rstan): Likewise.
* gnu/packages/django.scm (python-django): Likewise.
* gnu/packages/dlang.scm (ldc-bootstrap): Likewise.
* gnu/packages/finance.scm (ledger): Likewise.
* gnu/packages/glib.scm (glib): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
(go-1.14): Likewise.
* gnu/packages/kde-frameworks.scm (kcalendarcore): Likewise.
(kdelibs4support): Likewise.
* gnu/packages/kodi.scm (kodi): Likewise.
* gnu/packages/mail.scm (mu): Likewise.
* gnu/packages/perl.scm (perl-libtime-parsedate): Likewise.
* gnu/packages/python-xyz.scm (python-robotframework): Likewise.
(python-dparse): Likewise.
* gnu/packages/rrdtool.scm (rrdtool): Likewise.
* gnu/packages/statistics.scm (r-with-tests): Likewise.
* gnu/packages/vim.scm (vim): Likewise.
* gnu/packages/virtualization.scm (ganeti): Likewise.
* gnu/packages/vpn.scm (strongswan): Likewise.
* gnu/packages/xfce.scm (xfce4-panel): Likewise.
* gnu/packages/mate.scm (libmateweather): Use 'search-input-file' for
"share/zoneinfo/zone.tab".
2021-07-24 16:23:22 +02:00
fd8aea010f
gnu: python-pysam: Make the check phase honor the tests? argument.
...
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
2021-07-22 10:58:22 +03:00
877792a6a7
gnu: python-pysam: Update to 0.16.0.1.
...
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1.
[arguments]: Update custom 'check phase.
[propagated-inputs]: Replace htslib-1.9 with 1.10.
[native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10,
bcftools-1.9 with 1.10.
(bcftools-1.9): Replace with bcftools-1.10.
[native-inputs]: Replace htslib-1.9 with 1.10.
(samtools-1.9): Replace with samtools-1.10.
[inputs]: Replace htslib-1.9 with 1.10.
2021-07-22 10:57:41 +03:00
cc4906d13b
gnu: Add htslib-1.10.
...
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
2021-07-22 10:50:58 +03:00
309b38bed6
gnu: python-biopython: Update to 1.73.
...
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
2021-07-22 09:14:12 +03:00
73830b5da3
gnu: Add r-battenberg.
...
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
2021-07-21 13:36:08 +02:00
ed636babfa
gnu: Add r-ascat.
...
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
2021-07-21 13:36:08 +02:00
690df95d1a
gnu: Add nanosv.
...
* gnu/packages/bioinformatics.scm (nanosv): New variable.
2021-07-21 13:36:08 +02:00
2b665b8a49
gnu: Add python-pyvcf.
...
* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
2021-07-21 13:36:08 +02:00
086c6800cf
gnu: checkm: Rename and update to 1.1.3.
...
Renamed from python2-checkm-genome to checkm to better reflect its
status as standalone-application and support for Python 3.
* gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to…
(checkm): …here and update to 1.1.3.
[propagated-inputs]: Move to inputs.
[inputs]: Use Python 3 dependencies.
[home-page]: Point to real home-page.
2021-07-21 13:36:08 +02:00
18a02fe7ca
gnu: Add tombo.
...
* gnu/packages/bioinformatics.scm (tombo): New variable.
2021-07-21 13:36:07 +02:00
0e47fcced4
Merge branch 'master' into core-updates
2021-07-18 19:50:01 +02:00
ef79d6c5d6
gnu: Add ocaml-sqlite3.
...
* gnu/packages/ocaml.scm (ocaml-sqlite3): New variable.
(ocaml4.07-sqlite3): Inherit from ocaml-sqlite3.
* gnu/packages/bioinformatics.scm (pplacer): Also use package-with-ocaml4.07
with ocaml-sqlite3.
2021-07-05 16:54:11 +02:00
ebb8e44a4a
gnu: bioperl-minimal: Avoid top-level cross-module references.
...
This could lead to circular reference breakage.
* gnu/packages/bioinformatics.scm (bioperl-minimal): Move top-level
references to perl-* variables and their transitive inputs to
'arguments' and 'inputs'.
2021-07-01 17:13:13 +02:00
b17ee44212
gnu: Do not import (gnu packages commencement).
...
Line introduced in 4efbf56e53
2021-07-01 17:13:13 +02:00
9dea3f101f
Merge branch 'master' into core-updates
...
Conflicts:
gnu/packages/cups.scm
gnu/packages/python-web.scm
gnu/packages/web.scm
guix/build/maven/pom.scm
2021-06-23 18:45:21 +02:00
07d2c72d39
gnu: ensembl-vep: Use a source file-name.
...
* gnu/packages/bioinformatics.scm (ensembl-vep)[source]: Add a file-name
field.
2021-06-22 13:49:05 +03:00
44bccf414b
gnu: Add perl-cworld-dekker.
...
* gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
2021-06-22 08:40:56 +02:00
8a62d8685a
gnu: Add python-iced.
...
* gnu/packages/bioinformatics.scm (python-iced): New variable.
2021-06-21 13:02:39 +02:00
6f9a80b331
Merge branch 'master' into core-updates
...
Note: this merge actually changes the 'curl' and 'python-attrs' derivations,
as part of solving caf4a7a27712964df69a4604d43c0e
2021-06-19 17:38:47 +02:00
748d3a2b8a
gnu: Add python-cgatcore.
...
* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
2021-06-14 23:13:56 +02:00
ea0a51071e
gnu: Rename qtbase to qtbase-5.
...
This change was automated via the following command:
$ git ls-files | xargs sed -i 's/,qtbase)/,qtbase-5)/g'
$ git ls-files | xargs sed -i 's/inherit qtbase)/inherit qtbase-5)/g'
$ git ls-files | xargs sed -i 's/package-version qtbase)/package-version qtbase-5)/g'
$ git checkout etc # to clear some spurious changes
This is done so the qtbase package can be upgraded to version 6 in the
following commit.
2021-06-14 00:24:42 -04:00
ac51eb1125
gnu: pigx-sars-cov2-ww: Update to 0.0.2.
...
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.2.
[inputs]: Add wget.
2021-06-08 22:43:47 +02:00
c9e8e7b0bf
gnu: pigx-bsseq: Update to 0.1.5.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.5.
2021-06-08 16:35:17 +02:00
dd3698c1ac
gnu: python-hicmatrix: Update to 15.
...
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
[arguments]: Enabled tests. Remove 'relax-requirements phase.
[native-inputs]: Add python-pytest.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-06-08 16:35:17 +02:00
61bce4d143
gnu: python-mappy: Move to (gnu packages bioinformatics).
...
* gnu/packages/python-xyz.scm (python-mappy): Move to ...
* gnu/packages/bioinformatics.scm: ... here.
2021-06-08 09:50:55 +03:00
4a01e00a13
gnu: pigx-rnaseq: Update to 0.0.17.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.17.
[arguments]: Remove "use-latest-salmon" phase; add "set-timezone" phase.
[inputs]: Replace r-gprofiler with r-gprofiler2; add r-ggpubr and
python-deeptools.
[native-inputs]: Add tzdata.
2021-06-08 00:53:06 +02:00
be067c908c
gnu: pigx-rnaseq: Adjust to upgrade of salmon.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase
"use-latest-salmon".
2021-06-07 16:50:33 +02:00
bb38287570
gnu: salmon: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (salmon): Update to 1.4.0.
[arguments]: Remove unnecessary flags, add other soon-to-be-unnecessary flags;
remove "prepare-rapmap" phase, add "prepare-pufferfish" phase, add
"fix-error-message-in-tests" phase, simplify "use-system-libraries" phase.
[inputs]: Add curl and pufferfish sources; remove libdivsufsort and rapmap
sources.
2021-06-07 16:50:33 +02:00
9875dae429
gnu: macs: Update to 2.2.7.1.
...
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
2021-06-07 16:50:33 +02:00
1ace395f9c
gnu: libgff: Update to 2.0.0.
...
* gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0.
[home-page]: Update to new home.
2021-06-07 16:50:33 +02:00
176513f5f3
gnu: jellyfish: Update to 2.3.0.
...
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.3.0.
[arguments]: Disable SSE to avoid tuning to the build node's CPU.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Update.
2021-06-07 16:50:33 +02:00
1ac8f05103
gnu: multiqc: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.10.1.
[arguments]: Remove build phase "relax-requirements"; replace "check" phase.
[propagated-inputs]: Add python-coloredlogs, python-future, python-networkx,
and python-rich; remove python-nose.
[native-inputs]: Add python-pytest and the test suite.
2021-06-07 10:53:16 +02:00
a8c653f0fc
gnu: python-hic2cool: Update to 0.8.3.
...
* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.
[source]: Download using git-fetch.
[arguments]: Enable tests. Add phase to make test data writable.
[propagated-inputs]: Add python-h5py, python-numpy, python-pandas,
python-scipy.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-06-07 10:38:54 +03:00
8d59c262ad
Merge branch 'master' into core-updates
...
Conflicts:
gnu/local.mk
gnu/packages/algebra.scm
gnu/packages/bioinformatics.scm
gnu/packages/curl.scm
gnu/packages/docbook.scm
gnu/packages/emacs-xyz.scm
gnu/packages/maths.scm
gnu/packages/plotutils.scm
gnu/packages/python-web.scm
gnu/packages/python-xyz.scm
gnu/packages/radio.scm
gnu/packages/readline.scm
gnu/packages/tls.scm
gnu/packages/xml.scm
gnu/packages/xorg.scm
2021-06-06 21:16:32 +02:00
b65c02e2d3
gnu: freebayes: Update to 1.3.5.
...
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5.
[source]: Remove patch.
[arguments]: Adjust custom 'patch-source phase for changes in source.
[inputs]: Remove zlib.
* gnu/packages/patches/freebayes-devendor-deps.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2021-06-06 12:13:28 +03:00
d1e7b50dbf
gnu: python-cooler: Update to 0.8.11.
...
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11.
[arguments]: Add build phase "patch-tests"; replace "check" phase.
[native-inputs]: Add python-codecov, python-pytest-cov, and
python-pytest-flake8.
[propagated-inputs]: Add python-six and python-sparse.
2021-06-06 08:33:21 +02:00
f98837a6ba
gnu: pigx-rnaseq: Update to 0.0.13.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13.
[arguments]: Remove obsolete substitutions.
[inputs]: Remove fastqc and trim-galore; add hisat2 and fastp.
2021-06-05 09:12:39 +02:00
7382aa00b8
gnu: python-scanpy: Update to 1.7.2.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
2021-06-04 23:51:35 +02:00
b2459387b9
gnu: nanopolish: Set #:guile argument of 'wrap-script'.
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* gnu/packages/bioinformatics.scm
(nanopolish)[arguments]<#:phases>{wrap-programs}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
2d092a2afa
gnu: gess: Set #:guile argument of 'wrap-script'.
...
* gnu/packages/bioinformatics.scm
(gess)[arguments]<#:phases>{install}
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
c4989f7569
gnu: prinseq: Set #:guile argument of 'wrap-script'.
...
* gnu/packages/bioinformatics.scm
(prinseq)[arguments]<#:phases>{install}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
fadbac0ecc
gnu: proteinortho: Set #:guile argument of 'wrap-script'.
...
* gnu/packages/bioinformatics.scm
(proteinortho)[arguments]<#:phases>{wrap-programs}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
d06ae05808
gnu: Add pigx-sars-cov2-ww.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
2021-06-04 12:57:08 +02:00
0928e55266
gnu: Add fit-sne.
...
* gnu/packages/bioinformatics.scm (fit-sne): New variable.
2021-06-03 12:22:29 +02:00
011d586c2c
gnu: Add biobambam2.
...
* gnu/packages/bioinformatics.scm (biobambam2): New variable.
2021-06-02 13:54:15 +02:00
18e0081045
gnu: Add libmaus2.
...
* gnu/packages/bioinformatics.scm (libmaus2): New variable.
2021-06-02 13:54:15 +02:00
7ae2b1f2dc
gnu: Add bamutils.
...
* gnu/packages/bioinformatics.scm (bamutils): New variable.
2021-06-01 13:14:38 +02:00
f463f376e9
gnu: bits: Use git-version and git-file-name.
...
* gnu/packages/bioinformatics.scm (bits)[version]: Use git-version.
[source]: Use git-file-name.
2021-05-31 16:10:20 +02:00
d1e1c02e28
gnu: piranha: Use git-version.
...
* gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version.
2021-05-31 16:10:00 +02:00
8c033085cc
gnu: r-chipkernels: Use git-version and git-file-name.
...
* gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version.
[source]: Use git-file-name.
2021-05-31 16:09:35 +02:00
3acfbd4811
gnu: f-seq: Use git-version and git-file-name.
...
* gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version.
[source]: Use git-file-name.
2021-05-31 16:09:07 +02:00
09b50a6ec2
gnu: bismark: Use git-file-name.
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* gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name.
2021-05-31 16:08:47 +02:00
f383f9e311
gnu: filevercmp: Use git-version.
...
* gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind
"revision" in outer let.
2021-05-31 16:08:12 +02:00
a6e7afd4d5
gnu: r-spp: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-spp): Move from here...
* gnu/packages/bioconductor.scm (r-spp): ...to here.
2021-05-31 15:53:20 +02:00
b0ecd6cea9
gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1.
...
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit
outside of the package value.
[version]: Use git-version.
[source]: Use git-file-name.
2021-05-31 15:46:30 +02:00
c294c0d782
gnu: r-methylkit: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...
* gnu/packages/bioconductor.scm (r-methylkit): ...to here.
2021-05-31 15:39:49 +02:00
7ab44aeed6
gnu: r-copywriter: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-copywriter): Move from here...
* gnu/packages/bioconductor.scm (r-copywriter): ...to here.
2021-05-31 15:39:49 +02:00
36cb01066c
gnu: r-copyhelper: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-copyhelper): Move from here...
* gnu/packages/bioconductor.scm (r-copyhelper): ...to here.
[source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment.
2021-05-31 15:39:47 +02:00
31e50e1f48
gnu: r-chipseq: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-chipseq): Move from here...
* gnu/packages/bioconductor.scm (r-chipseq): ...to here.
2021-05-31 15:39:00 +02:00
0eaa75c811
gnu: r-rhdf5: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
2021-05-31 15:39:00 +02:00
cc1dbea883
gnu: r-annotationfilter: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here...
* gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.
2021-05-31 15:39:00 +02:00
67e99369c1
gnu: r-rhdf5filters: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.
2021-05-31 15:39:00 +02:00
b6e84d30eb
gnu: r-tximport: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-tximport): Move from here...
* gnu/packages/bioconductor.scm (r-tximport): ...to here.
2021-05-31 15:39:00 +02:00
bf8f502956
gnu: r-mutationalpatterns: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here...
* gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.
2021-05-31 15:39:00 +02:00
7360dea624
gnu: r-rcas: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-rcas): Move from here...
* gnu/packages/bioconductor.scm (r-rcas): ...to here.
2021-05-31 15:39:00 +02:00
45b6db4fb4
gnu: r-bamsignals: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Move from here...
* gnu/packages/bioconductor.scm (r-bamsignals): ...to here.
2021-05-31 15:38:59 +02:00
043c309d15
gnu: r-rhtslib: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here...
* gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
2021-05-31 15:38:59 +02:00
e0c81584ea
gnu: r-zlibbioc: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here...
* gnu/packages/bioconductor.scm (r-zlibbioc): ...to here.
2021-05-31 15:38:58 +02:00
0006a66415
gnu: r-seqlogo: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Move from here...
* gnu/packages/bioconductor.scm (r-seqlogo): ...to here.
2021-05-31 15:38:21 +02:00
c2a18aee16
gnu: r-motifrg: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-motifrg): Move from here...
* gnu/packages/bioconductor.scm (r-motifrg): ...to here.
2021-05-31 15:38:00 +02:00
621aa3b442
gnu: r-sva: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-sva): Move from here...
* gnu/packages/bioconductor.scm (r-sva): ...to here.
2021-05-31 15:38:00 +02:00
900ef8fb1e
gnu: r-protgenerics: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-protgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-protgenerics): ...to here.
2021-05-31 15:38:00 +02:00
720d2694a5
gnu: r-mzr: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-mzr): Move from here...
* gnu/packages/bioconductor.scm (r-mzr): ...to here.
2021-05-31 15:38:00 +02:00
88cf24febb
gnu: r-ensembldb: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Move from here...
* gnu/packages/bioconductor.scm (r-ensembldb): ...to here.
2021-05-31 15:37:59 +02:00
fea33b9d1e
gnu: r-biovizbase: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-biovizbase): Move from here...
* gnu/packages/bioconductor.scm (r-biovizbase): ...to here.
2021-05-31 15:37:59 +02:00
8d4311bb8e
gnu: r-vsn: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-vsn): Move from here...
* gnu/packages/bioconductor.scm (r-vsn): ...to here.
2021-05-31 15:37:59 +02:00
96ae9822c4
gnu: r-affyio: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-affyio): Move from here...
* gnu/packages/bioconductor.scm (r-affyio): ...to here.
2021-05-31 15:37:59 +02:00
8182e6a6fd
gnu: r-organismdbi: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-organismdbi): Move from here...
* gnu/packages/bioconductor.scm (r-organismdbi): ...to here.
2021-05-31 15:37:59 +02:00
d1ea2b7c8b
gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here...
* gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here.
2021-05-31 15:37:59 +02:00
0b5b41c561
gnu: r-genomicfiles: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfiles): ...to here.
2021-05-31 15:37:59 +02:00
ff65fa90d2
gnu: r-complexheatmap: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here...
* gnu/packages/bioconductor.scm (r-complexheatmap): ...to here.
2021-05-31 15:37:59 +02:00
84019edf38
gnu: r-gage: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-gage): Move from here...
* gnu/packages/bioconductor.scm (r-gage): ...to here.
2021-05-31 15:37:59 +02:00
d0a5503752
gnu: r-keggrest: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-keggrest): Move from here...
* gnu/packages/bioconductor.scm (r-keggrest): ...to here.
2021-05-31 15:37:58 +02:00
22cda2e432
gnu: r-affy: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-affy): Move from here...
* gnu/packages/bioconductor.scm (r-affy): ...to here.
2021-05-31 15:37:58 +02:00
32ae36e96f
gnu: r-fastseg: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-fastseg): Move from here...
* gnu/packages/bioconductor.scm (r-fastseg): ...to here.
2021-05-31 15:37:58 +02:00
9644745692
gnu: r-annotationhub: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-annotationhub): Move from here...
* gnu/packages/bioconductor.scm (r-annotationhub): ...to here.
2021-05-31 15:37:58 +02:00
dfe6224f5f
gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here...
* gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here.
2021-05-31 15:37:58 +02:00
f6f43a2d40
gnu: r-edaseq: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-edaseq): Move from here...
* gnu/packages/bioconductor.scm (r-edaseq): ...to here.
2021-05-31 15:37:58 +02:00
ef954bb488
gnu: r-deseq: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-deseq): Move from here...
* gnu/packages/bioconductor.scm (r-deseq): ...to here.
2021-05-31 15:37:58 +02:00
bb118f20fe
gnu: r-aroma-light: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-aroma-light): Move from here...
* gnu/packages/bioconductor.scm (r-aroma-light): ...to here.
2021-05-31 15:37:58 +02:00
7756e08b44
gnu: r-mzid: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-mzid): Move from here...
* gnu/packages/bioconductor.scm (r-mzid): ...to here.
2021-05-31 15:37:58 +02:00
ad46c8aa7f
gnu: r-pcamethods: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-pcamethods): Move from here...
* gnu/packages/bioconductor.scm (r-pcamethods): ...to here.
2021-05-31 15:37:57 +02:00
d7fa9c1ffd
gnu: r-genomationdata: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-genomationdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomationdata): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment.
2021-05-31 15:37:55 +02:00
f8fe5497c7
gnu: r-genomation: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-genomation): Move from here...
* gnu/packages/bioconductor.scm (r-genomation): ...to here.
2021-05-31 15:36:32 +02:00
f3b50aa4fd
gnu: r-go-db: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-go-db): Move from here...
* gnu/packages/bioconductor.scm (r-go-db): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'annotation.
2021-05-31 15:35:53 +02:00
14fb30e5f6
gnu: r-seqpattern: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Move from here...
* gnu/packages/bioconductor.scm (r-seqpattern): ...to here.
2021-05-31 15:35:30 +02:00
b832fddbfc
gnu: r-impute: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-impute): Move from here...
* gnu/packages/bioconductor.scm (r-impute): ...to here.
2021-05-31 15:34:45 +02:00
4f030cc0db
gnu: r-msnbase: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-msnbase): Move from here...
* gnu/packages/bioconductor.scm (r-msnbase): ...to here.
2021-05-31 15:34:44 +02:00
8c7c78bfce
gnu: r-msnid: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-msnid): Move from here...
* gnu/packages/bioconductor.scm (r-msnid): ...to here.
2021-05-31 15:34:44 +02:00
537d48d869
gnu: r-bsgenome: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome): ...to here.
2021-05-31 15:34:44 +02:00
90bbab5cff
gnu: r-topgo: Move to (gnu packages bioconductor).
...
* gnu/packages/bioinformatics.scm (r-topgo): Move from here...
* gnu/packages/bioconductor.scm (r-topgo): ...to here.
2021-05-31 15:34:44 +02:00
f78ff75b41
gnu: r-genomicfeatures: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here.
2021-05-31 15:34:44 +02:00
a88230a1bc
gnu: r-rtracklayer: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here...
* gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.
2021-05-31 15:34:44 +02:00
ca1a015777
gnu: r-genomicalignments: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here...
* gnu/packages/bioconductor.scm (r-genomicalignments): ...to here.
2021-05-31 15:34:39 +02:00
e3cde9aaf8
gnu: Add mosaicatcher.
...
* gnu/packages/patches/mosaicatcher-unbundle-htslib.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
2021-05-29 07:26:15 +02:00
6417b97c7e
Revert "gnu: Add mosaicatcher."
...
mosaicatcher-unbundle-htslib.patch is missing.
This reverts commit b1ae0f30d8
2021-05-29 01:21:14 +01:00
Ludovic Courtès
Ricardo Wurmus
Vagrant Cascadian
Julien Lepiller
Efraim Flashner
Mathieu Othacehe
Felix Gruber
Lars-Dominik Braun
Charles
zimoun
Marius Bakke
Tobias Geerinckx-Rice
Maxim Cournoyer
Mădălin Ionel Patrașcu
Roel Janssen
Maxime Devos
Christopher Baines