44db90b39f
gnu: python-loompy: Do not set PYTHONPATH.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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
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.
...
* 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.
...
* 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.
...
* 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
cde035e67f
gnu: r-gqtlstats: Update to 1.21.3.
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.21.3.
2020-12-09 12:12:48 +01:00
6a4818716d
gnu: r-gqtlbase: Update to 1.21.1.
...
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.21.1.
[arguments]: Add phase to patch broken NAMESPACE file.
2020-12-09 12:12:48 +01:00
970984237a
gnu: r-biocviews: Update to 1.58.1.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.1.
Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
2020-12-09 12:12:47 +01:00
53affb349a
gnu: r-rhdf5: Update to 2.34.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.34.0.
[propagated-inputs]: Add r-rhdf5filters.
[arguments]: Avoid to have a plain directory on the list of libraries to
link.
Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
2020-12-09 12:12:46 +01:00
86fcceeae1
gnu: Add r-rhdf5filters.
...
* gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable.
2020-12-09 12:12:46 +01:00
60ad3c7b3b
gnu: r-genomationdata: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.22.0.
2020-12-09 12:12:46 +01:00
e707820442
gnu: r-sushi: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.28.0.
2020-12-09 12:12:45 +01:00
83129edfb7
gnu: r-gwascat: Update to 2.22.0.
...
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.22.0.
[propagated-inputs]: Add r-biocfilecache, r-readr, r-snpstats, and
r-variantannotation; remove r-biocgenerics, r-ggplot2, r-rsamtools, and
r-rtracklayer.
2020-12-09 12:12:45 +01:00
717e53fdc0
gnu: r-gviz: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.34.0.
2020-12-09 12:12:45 +01:00
0a8d08e887
gnu: r-ldblock: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.20.0.
2020-12-09 12:12:45 +01:00
494010ad3e
gnu: r-erma: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.6.0.
2020-12-09 12:12:45 +01:00
6e338901bf
gnu: r-snpstats: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.40.0.
2020-12-09 12:12:45 +01:00
74a11b21be
gnu: r-ggbio: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.38.0.
2020-12-09 12:12:45 +01:00
3c6eecdeed
gnu: r-biovizbase: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.38.0.
2020-12-09 12:12:45 +01:00
6e182c237a
gnu: r-organismdbi: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.32.0.
2020-12-09 12:12:44 +01:00
06fe3b7a53
gnu: r-ensembldb: Update to 2.14.0.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.0.
2020-12-09 12:12:44 +01:00
8962a13afe
gnu: r-dirichletmultinomial: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.32.0.
2020-12-09 12:12:44 +01:00
4ef1e375b4
gnu: r-complexheatmap: Update to 2.6.2.
...
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.6.2;
[propagated-inputs]: Add r-cairo, r-digest, r-iranges, r-matrixstats, and
r-s4vectors.
2020-12-09 12:12:44 +01:00
0fde2f9ad2
gnu: r-genomicfiles: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.26.0.
[propagated-inputs]: Add r-matrixgenerics.
2020-12-09 12:12:44 +01:00
78cadd0fef
gnu: r-gage: Update to 2.40.0.
...
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.0.
2020-12-09 12:12:44 +01:00
143437c623
gnu: r-keggrest: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.0.
2020-12-09 12:12:44 +01:00
b6dd0722c8
gnu: r-fastseg: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.36.0.
2020-12-09 12:12:44 +01:00
a9dc755e67
gnu: r-annotationhub: Update to 2.22.0.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.0.
2020-12-09 12:12:43 +01:00
3becce3ff3
gnu: r-interactivedisplaybase: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.28.0.
2020-12-09 12:12:43 +01:00
Maxim Cournoyer
zimoun
Ricardo Wurmus
Marius Bakke
Roel Janssen