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Author SHA1 Message Date
Navid Afkhami
5a293d0830
gnu: Add python-baltica. 
* gnu/packages/bioinformatics.scm (python-baltica): New variable.
 2023-08-01 16:24:29 +02:00
Navid Afkhami
c963ba2ebb
gnu: Add python-liana-py. 
* gnu/packages/bioinformatics.scm (python-liana-py): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-07-31 12:21:12 +02:00
Navid Afkhami
fe3e05d8b3
gnu: python-decoupler-py: Update to 1.5.0-1.459b235. 
* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to
1.5.0-1.459b235.
[arguments]: Disable two more tests.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-07-31 12:06:21 +02:00
Tobias Geerinckx-Rice
789f7e9a3d
gnu: fuse@3: Bind to default FUSE variable. 
* gnu/packages/linux.scm (fuse): Rename this…
(fuse-2): …to this, and…
(fuse-3): …rename this…
(fuse): …to this!
(fuse-static): Rename this…
(fuse-2-static): …to this.
Adjust all users.
 2023-07-23 02:00:00 +02:00
Efraim Flashner
0867cdc514
gnu: newick-utils: Skip tests when cross-compiling. 
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Adjust
 #: tests? to skip tests when cross-compiling.
 2023-07-21 13:19:33 +03:00
Nicolas Goaziou
e6fc11ae07
gnu: discrover: Fix build. 
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add
TEXLIVE-FORLOOP, TEXLIVE-LISTOFITEMS, TEXLIVE-READARRAY.
 2023-07-18 18:16:48 +02:00
Nicolas Goaziou
7a18bd9e74
gnu: Rationalize texlive-updmap.cfg and texlive-tiny inputs. 
TEXLIVE-UPDMAP.CFG and TEXLIVE-TINY should only be used as native inputs.
Also remove texlive packages already provided by them.

* doc/build.scm (pdf-manual):
* gnu/packages/algebra.scm (pari-gp):
* gnu/packages/bioinformatics.scm (discrover):
(phyml):
(velvet):
* gnu/packages/chemistry.scm (yaehmop):
* gnu/packages/chez.scm (stex-bootstrap):
(chez-web):
(chez-sockets):
* gnu/packages/cran.scm (r-prereg):
* gnu/packages/docbook.scm (dblatex):
* gnu/packages/emacs-xyz.scm (emacs-auctex):
* gnu/packages/engineering.scm (fastcap):
* gnu/packages/fsf.scm (book-faif):
* gnu/packages/graphviz.scm (dot2tex):
* gnu/packages/maths.scm (hypre):
* gnu/packages/ocaml.scm (unison):
(ocaml-bibtex2html):
* gnu/packages/plotutils.scm (asymptote):
* gnu/packages/python-xyz.scm (python-nbconvert):
(python-pypandoc):
* gnu/packages/radio.scm (gnuradio):
(libosmo-dsp):
* gnu/packages/statistics.scm (r-with-tests):
* gnu/packages/tex.scm (texlive-makecmds):
(texlive-innerscript):
(teximpatient):
(texlive-xkeyval): Remove texlive packages already provided by
TEXLIVE-UPDMAP.CFG.  Don't add TEXLIVE-TINY or TEXLIVE-UPDMAP.CFG as inputs.
 2023-07-18 18:16:47 +02:00
Nicolas Goaziou
88a3b237f5
gnu: phyml: Fix build. 
* gnu/packages/bioinformatics.scm (phyml)[native-inputs]: Add
TEXLIVE-INFWARERR, TEXLIVE-KVOPTIONS and TEXLIVE-PDFTEXCMDS.
 2023-07-18 18:16:45 +02:00
Nicolas Goaziou
1e92db8927
gnu: velvet: Improve package style. 
* gnu/packages/bioinformatics.scm (velvet)[arguments]: Use G-expressions.
[native-inputs]: Remove label.
 2023-07-18 18:16:42 +02:00
Nicolas Goaziou
42500f1aad
gnu: velvet: Fix error when building documentation. 
* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add TEXLIVE-GRFEXT,
TEXLIVE-INFWARERR, TEXLIVE-KVOPTIONS and TEXLIVE-KPDFTEXCMDS.
 2023-07-18 18:16:41 +02:00
Nicolas Goaziou
95e4d69805
gnu: texlive-latex-examplep -> texlive-examplep. 
* gnu/packages/tex.scm (texlive-examplep): New variable.
(texlive-latex-examplep): Deprecate variable.
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use new name.
 2023-07-18 18:11:02 +02:00
Nicolas Goaziou
8cfcce5194
gnu: texlive-latex-verbatimbox -> texlive-verbatimbox. 
* gnu/packages/tex.scm (texlive-verbatimbox): New variable.
(texlive-latex-verbatimbox): Deprecate variable.
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use new name.
 2023-07-18 18:11:02 +02:00
Nicolas Goaziou
76819a9655
gnu: texlive-fonts-ec -> texlive-ec. 
* gnu/packages/tex.scm (texlive-ec): New variable.
(texlive-fonts-ec): Deprecate variable.
(lyx):
(biber):
* gnu/packages/python-xyz.scm (python-pypandoc):
* gnu/packages/statistics.scm (r-with-tests):
* doc/build.scm (pdf-manual):
* gnu/packages/bioinformatics.scm (discrover):
(phyml):
(velvet):
* gnu/packages/chemistry.scm (yaehmop):
* gnu/packages/chez.scm (stex-bootstrap):
* gnu/packages/ocaml.scm (unison):
(ocaml-bibtex2html):
* gnu/packages/plotutils.scm (asymptote): Use new name.
 2023-07-18 18:10:48 +02:00
Nicolas Goaziou
7af4d29ace
gnu: texlive-latex-psfrag -> texlive-psfrag. 
* gnu/packages/tex.scm (texlive-psfrag): New variable.
(texlive-latex-psfrag): Deprecate variable.
(texlive-pstool):
* gnu/packages/bioinformatics.scm (phyml): Use new name.
 2023-07-18 18:10:39 +02:00
Nicolas Goaziou
b42e997e85
gnu: texlive-latex-natbib -> texlive-natbib. 
* gnu/packages/tex.scm (texlive-natbib): New variable.
(texlive-latex-natbib): Deprecate variable.
(texlive-apacite):
* gnu/packages/bioinformatics.scm (discrover):
* gnu/packages/maths.scm (hypre): Use new name.
 2023-07-18 18:10:38 +02:00
宋文武
a6eb936d28
gnu: newick-utils: Skip tests on riscv64-linux. 
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Skip tests
when building on riscv64-linux.
 2023-07-18 20:23:42 +08:00
Christopher Baines
54a74d35e6
gnu: Hide python-bcbio-gff/biopython-1.73. 
To avoid the ambiguous package specification.

* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73): Hide
package.
 2023-07-17 09:06:34 +01:00
Ricardo Wurmus
a065e12f82
gnu: r-pando: Relax requirements. 
* gnu/packages/bioinformatics.scm (r-pando)[arguments]: Patch DESCRIPTION
file.
 2023-07-15 11:11:02 +02:00
Tobias Geerinckx-Rice
2195645725
gnu: bwa-pssm: Update home page. 
* gnu/packages/bioinformatics.scm (bwa-pssm)[home-page]: Update.
 2023-07-09 02:00:17 +02:00
Tobias Geerinckx-Rice
6f80e25f35
gnu: blasr-libcpp, blasr: Use Web Archived home pages. 
* gnu/packages/bioinformatics.scm (blasr-libcpp, blasr)[home-page]:
 Refer to Web Archive.
 2023-07-09 02:00:10 +02:00
Ricardo Wurmus
2794caed7c
gnu: Add r-numbat. 
* gnu/packages/bioinformatics.scm (r-numbat): New variable.
 2023-07-12 21:34:07 +02:00
Ricardo Wurmus
3b524cde71
gnu: Add r-bpcells. 
* gnu/packages/bioinformatics.scm (r-bpcells): New variable.
 2023-07-12 16:45:42 +02:00
Ricardo Wurmus
de3b8684e9
gnu: r-pando: Fix hash. 
* gnu/packages/bioinformatics.scm (r-pando)[source]: Update hash.
 2023-07-06 23:29:05 +02:00
Ricardo Wurmus
df5bf65f26
gnu: bismark: Update to 0.24.1. 
* gnu/packages/bioinformatics.scm (bismark): Update to 0.24.1.
[source]: Delete bundled plot.ly.
[arguments]: Use plain list; remove trailing #T from build phases; adjust
'replace-plotly.js phase to account for use of script tags; adjust 'install
phase to install documentation in markdown format; add 'configure phase for
replacing references to tools.
[inputs]: Add bowtie, hisat2, minimap2, and samtools.
 2023-07-06 23:29:05 +02:00
Ricardo Wurmus
c66e5ef5f9
gnu: cutadapt: Update to 4.0. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Disable a single test; remove 'always-cythonize build phase; add
phase 'fix-test.
[native-inputs]: Add python-pytest-mock and python-pytest-timeout.
 2023-07-03 16:37:45 +02:00
Ricardo Wurmus
cb15c60d35
gnu: python-dnaio: Update to 0.10.0. 
* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.10.0.
[arguments]: Disable tests, because they don't exist.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-setuptools-scm; move python-xopen from here...
[propagated-inputs]: ...to here.
 2023-07-03 16:36:53 +02:00
Navid Afkhami
669f0eaed6
gnu: Add r-dtmm. 
* gnu/packages/bioinformatics.scm (r-dtmm): New variable.
 2023-07-03 13:42:47 +02:00
Navid Afkhami
94ac93042f
gnu: Add rscape. 
* gnu/packages/bioinformatics.scm (rscape): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-06-29 22:25:35 +02:00
Ricardo Wurmus
10ff8ff4b5
gnu: r-pando: Update to 1.0.5. 
* gnu/packages/bioinformatics.scm (r-pando): Update to 1.0.5.
[propagated-inputs]: Remove r-brms and r-xgboost; add r-grr and
r-matrixgenerics.
 2023-06-29 12:01:22 +02:00
Efraim Flashner
7f3c6d3b3b
gnu: sambamba: Fix building. 
* gnu/packages/bioinformatics.scm (sambamba)[native-inputs]: Remove
ld-gold-wrapper, bintutils-gold. Remove input labels.
 2023-06-22 12:19:49 +03:00
Christopher Baines
7b535eb29b
gnu: bioruby: Update to 2.0.4. 
* gnu/packages/bioinformatics.scm (bioruby): Update to 2.0.4.
[arguments]: Update style.
 2023-06-20 22:04:51 +01:00
Navid Afkhami
74443c30f3
gnu: Add python-mudata. 
* gnu/packages/bioinformatics.scm (python-mudata): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-06-09 17:09:38 +02:00
Navid Afkhami
c348b1be38
gnu: Add python-mofax. 
* gnu/packages/bioinformatics.scm (python-mofax): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-06-09 16:56:22 +02:00
Navid Afkhami
f056d4f168
gnu: Add python-decoupler-py. 
* gnu/packages/bioinformatics.scm (python-decoupler-py): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
 2023-06-06 21:35:37 +02:00
Ricardo Wurmus
4f2ec0f2d1
gnu: python-bulkvis: Reference upstream issue. 
* gnu/packages/bioinformatics.scm (python-bulkvis)[arguments]: Add comment
with link to upstream issue for bokeh compatibility patch.
 2023-06-05 17:20:52 +02:00
Navid Afkhami
6559adea29
gnu: Add python-bulkvis. 
* gnu/packages/bioinformatics.scm (python-bulkvis): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2023-06-05 17:11:15 +02:00
Navid Afkhami
91e75bb35f
gnu: Add python-readpaf. 
* gnu/packages/bioinformatics.scm (python-readpaf): New variable.
 2023-06-05 17:11:14 +02:00
Ricardo Wurmus
c11b92a8aa
gnu: Add r-singlet. 
* gnu/packages/bioinformatics.scm (r-singlet): New variable.
 2023-06-02 21:18:26 +02:00
Navid Afkhami
f09944461f
gnu: Add python-cell2cell. 
* gnu/packages/bioinformatics.scm (python-cell2cell): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-06-02 19:54:27 +02:00
Ricardo Wurmus
341b4b2a97
gnu: Add java-maxent. 
* gnu/packages/bioinformatics.scm (java-maxent): New variable.
 2023-06-02 11:34:17 +02:00
Ricardo Wurmus
d411b7d5e7
gnu: Add python-pyani. 
* gnu/packages/bioinformatics.scm (python-pyani): New variable.
 2023-06-01 20:48:17 +02:00
Ricardo Wurmus
525ef60ff4
gnu: Add python-illumina-utils. 
* gnu/packages/bioinformatics.scm (python-illumina-utils): New variable.
 2023-06-01 20:48:17 +02:00
Ricardo Wurmus
ced6e0fe94
gnu: Add python-ete3. 
* gnu/packages/bioinformatics.scm (python-ete3): New variable.
 2023-06-01 14:10:04 +02:00
Ricardo Wurmus
60b71b0db4
gnu: Add python-gseapy. 
* gnu/packages/bioinformatics.scm (python-gseapy): New variable.
 2023-05-26 14:36:14 +02:00
Ricardo Wurmus
980d2cd73b
gnu: java-picard-1.113: Drop input package labels. 
* gnu/packages/bioinformatics.scm (java-picard-1.113)[inputs]: Drop labels.
 2023-05-19 13:12:29 +02:00
Ricardo Wurmus
1baf94dbbe
gnu: java-picard-1.113: Drop trailing #T from build phases. 
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Remove
trailing #T from build phases.
 2023-05-19 13:12:29 +02:00
Ricardo Wurmus
69d74e35b2
gnu: discrover: Remove package labels. 
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Remove package
labels.
 2023-05-14 13:48:01 +02:00
Ricardo Wurmus
8ec227471a
gnu: diamond: Update to 2.1.6. 
* gnu/packages/bioinformatics.scm (diamond): Update to 2.1.6.
[arguments]: Do not disable tests; pass configure flag to avoid SSE4 and AVX2
in the interest of compatibility.
[license]: Set to GPLv3+.
 2023-05-14 13:39:05 +02:00
Ricardo Wurmus
6754eb339c
gnu: delly: Simplify. 
* gnu/packages/bioinformatics.scm (delly)[source]: Simplify snippet.
[arguments]: Do not use quasiquote; simplify 'install-templates phase.
 2023-05-14 13:29:34 +02:00
Ricardo Wurmus
302e7b7820
gnu: python-pybigwig: Update to 0.3.22. 
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.22.
[source]: Simplify snippet.
[arguments]: Explicitly disable tests; simplify 'link-with-libBigWig phase.
[build-system]: Use pyproject-build-system.
 2023-05-14 13:26:21 +02:00
Ricardo Wurmus
7e303658d7
gnu: codingquarry: Use G-expression. 
* gnu/packages/bioinformatics.scm (codingquarry)[arguments]: Use G-expression
to simplify 'install phase.  Install files to /share/codingquarry prefix.
[native-search-paths]: Adjust prefix.
[native-inputs]: Move python-2 from here...
[inputs]: ...to here.
 2023-05-14 13:21:59 +02:00
Ricardo Wurmus
68ccd1a0d8
gnu: blast+: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (blast+): Update to 2.14.0.
[arguments]: Remove trailing #T from build phases; let WHICH* return #FALSE on
failure; use G-expression.
[inputs]: Drop package labels.
 2023-05-14 12:58:22 +02:00
Ricardo Wurmus
e4ca1bcea5
gnu: jamm: Use G-expression. 
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Use G-expression.
 2023-05-12 22:50:08 +02:00
Ricardo Wurmus
662e2e82b1
gnu: arriba: Use SEARCH-INPUT-FILE and -DIRECTORY. 
* gnu/packages/bioinformatics.scm (arriba)[arguments]:
Use SEARCH-INPUT-DIRECTORY and SEARCH-INPUT-FILE; use G-expression; drop
trailing #T from build phases.
 2023-05-12 22:40:18 +02:00
Ricardo Wurmus
001d9b1c64
gnu: multichoose: Clean up. 
* gnu/packages/bioinformatics.scm (multichoos): Fix indentation.
[arguments]: Use G-expression.
 2023-05-12 22:33:44 +02:00
Ricardo Wurmus
6d72af0747
gnu: samblaster: Update to 0.1.26. 
* gnu/packages/bioinformatics.scm (samblaster): Update to 0.1.26.
 2023-05-12 22:31:22 +02:00
Ricardo Wurmus
6331e41cde
gnu: samblaster: Simplify. 
* gnu/packages/bioinformatics.scm (samblaster): Fix indentation.
[arguments]: Use G-expression; drop trailing #T from 'install phase.
[description]: Use double spacing between all sentences.
 2023-05-12 22:29:38 +02:00
Ricardo Wurmus
7da3ca1bd7
gnu: methyldackel: Update to 0.6.1. 
* gnu/packages/bioinformatics.scm (methyldackel): Update to 0.6.1.
[arguments]: Set LIBBIGWIG variable instead of patching Makefile.
[inputs]: Replace htslib-1.9 with htslib.
 2023-05-12 22:27:17 +02:00
Ricardo Wurmus
7a199bb74c
gnu: methyldackel: Simplify arguments. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Use list, drop
argument list.
[native-inputs]: Drop package label.
 2023-05-12 22:24:30 +02:00
Ricardo Wurmus
5d446e439d
gnu: phast: Simplify by using G-expression. 
* gnu/packages/bioinformatics.scm (phast)[arguments]: Use G-expression and
drop trailing #T from build phases.
 2023-05-12 22:23:23 +02:00
Ricardo Wurmus
fac8721bfd
gnu: ribotaper: Simplify with G-expression. 
* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Use G-expression and
drop trailing #T from build phase.
 2023-05-12 22:21:14 +02:00
Ricardo Wurmus
0e20ed322d
gnu: sra-tools: Do link with libxml2. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use G-expression for
clarity; drop trailing #T from build phases; modify 'configure phase to
dynamically link with libxml2.
[inputs]: Drop package labels; add libxml2.
 2023-05-12 21:54:01 +02:00
Ricardo Wurmus
8ba3bf6564
gnu: ncbi-vdb: Ensure that vdb-sqlite is installed. 
The most important change here is the addition of the 'install-libs phase.
All other changes are just the result of switching to G-expressions.

* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add 'install-libs
phase; use G-expression; drop trailing #T from build phases.
[inputs]: Drop package labels.
 2023-05-12 21:51:41 +02:00
Mădălin Ionel Patrașcu
263f235cd0
gnu: Add python-mgatk. 
* gnu/packages/bioinformatics.scm (python-mgatk): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2023-05-12 15:30:44 +02:00
Ricardo Wurmus
42e9e8ba2e
gnu: Add homer. 
* gnu/packages/bioinformatics.scm (homer): New variable.
 2023-05-08 18:50:38 +02:00
Ricardo Wurmus
94d0efffb3
Revert "gnu: Add python-gimmemotifs." 
This reverts commit dc8b3ebe5d.

python-gimmemotifs is not usable without proprietary third-party tools.
 2023-05-05 22:34:30 +02:00
Ricardo Wurmus
dc8b3ebe5d
gnu: Add python-gimmemotifs. 
* gnu/packages/bioinformatics.scm (python-gimmemotifs): New variable.
 2023-05-05 15:39:29 +02:00
Ricardo Wurmus
931650212a
gnu: Add python-biofluff. 
* gnu/packages/bioinformatics.scm (python-biofluff): New variable.
 2023-05-05 15:39:29 +02:00
Ricardo Wurmus
0b5088a2a3
gnu: Add python-genomepy. 
* gnu/packages/bioinformatics.scm (python-genomepy): New variable.
 2023-05-05 15:39:29 +02:00
Ricardo Wurmus
181714e5f8
gnu: Add python-logomaker. 
* gnu/packages/bioinformatics.scm (python-logomaker): New variable.
 2023-05-05 15:39:29 +02:00
Ricardo Wurmus
7dc853269f
gnu: python-pyfaidx: Update to 0.7.2.1. 
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.7.2.1.
[build-system]: Use pyproject-build-system.
[arguments]: Ignore tests that require large downloads.
[native-inputs]: Remove python-six; add python-fsspec, python-pytest,
python-pytest-cov, python-mock, and python-numpy.
 2023-05-05 15:39:28 +02:00
Mădălin Ionel Patrașcu
00051e8839
gnu: python-screed: Update to 1.1.2. 
* gnu/packages/bioinformatics.scm (python-screed): Update to 1.1.2.
[build-system]: Use pyproject-build-system.
[native-inputs]: Remove python-pytest.
[inputs]: Remove python-bz2file.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-05-04 19:28:23 +02:00
Navid Afkhami
5daf470e4f
gnu: Add python-goatools. 
* gnu/packages/bioinformatics.scm (python-goatools): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2023-05-04 19:22:04 +02:00
Ricardo Wurmus
3f02f7d937
gnu: pigx-sars-cov-2: Update to 0.0.9. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.9.
 2023-05-03 17:02:02 +02:00
Ricardo Wurmus
83a6ca3c60
gnu: Add fanc. 
* gnu/packages/bioinformatics.scm (fanc): New variable.
 2023-05-03 11:59:54 +02:00
Ricardo Wurmus
2b08f6874e
gnu: r-tictoc: Update to 1.2. 
* gnu/packages/bioinformatics.scm (r-tictoc): Update to 1.2.
 2023-04-29 20:28:08 +02:00
Ricardo Wurmus
5775bbdd4b
gnu: gdcm: Disable dependent tests. 
* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Disable tests that depend
on the output of a disabled test.
 2023-04-27 16:23:22 +02:00
Ricardo Wurmus
fa685c87ea
gnu: freebayes: Update to 1.3.7. 
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.7.
[arguments]: Do not use "grep -P" in tests; drop trailing #T.
 2023-04-27 11:40:09 +02:00
Ricardo Wurmus
133957f7bb
gnu: vcflib: Use libwfa2.pc. 
* gnu/packages/bioinformatics.scm (vcflib)[source]: Use pkg-config to look for
libwfa2.
[inputs]: Move wfa2-lib from here...
[propagated-inputs]: ...to here.
[arguments]: Drop WFA_LINK_LIBRARIES option; fix typo in build phase name;
patch IntervalTree.h includes; add libwfa2 to pkg-config file.
 2023-04-27 11:38:16 +02:00
Ricardo Wurmus
479f2558fe
gnu: wfa2-lib: Install pkg-config file. 
* gnu/packages/bioinformatics.scm (wfa2-lib)[arguments]: Install libwfa2.pc.
 2023-04-27 11:37:36 +02:00
Ricardo Wurmus
9d82c475a3
gnu: express: Adjust bamtools location. 
* gnu/packages/bioinformatics.scm (express)[arguments]: Modify location of
libbamtools.so in 'use-shared-boost-libs-and-set-bamtools-paths; drop trailing
 #T.
 2023-04-27 09:25:26 +02:00
Ricardo Wurmus
bb385f2472
gnu: python-dendropy: Fix build. 
* gnu/packages/bioinformatics.scm (python-dendropy)[native-inputs]: Add
python-pytest.
[arguments]: Add phase 'python-compatibility; remove 'skip-broken-tests; add
 #:test-flags; do not delete test files.
[build-system]: Use pyproject-build-system.
 2023-04-26 22:53:26 +02:00
Ricardo Wurmus
4598928a90
gnu: cwltool: Use pyproject-build-system. 
"setup.py install is deprecated. Use build and pip and other standards-based
tools."  It then falls back to attempting to install packages via pip.

* gnu/packages/bioinformatics.scm (cwltool)[build-system]: Use
pyproject-build-system.
 2023-04-25 21:18:36 +02:00
Ricardo Wurmus
92a903499b
gnu: python-schema-salad: Use pyproject-build-system. 
The python-build-system fails with "setuptools.installer is
deprecated. Requirements should be satisfied by a PEP 517 installer."  This,
in turn, causes all Python packages to be ignored and "pip install" to be
invoked for them.

* gnu/packages/bioinformatics.scm (python-schema-salad)[build-system]: Use
pyproject-build-system.
 2023-04-25 21:18:35 +02:00
Ricardo Wurmus
5a1b246736
gnu: adapterremoval: Update to 2.3.3. 
* gnu/packages/bioinformatics.scm (adapterremoval): Update to 2.3.3.
[arguments]: Simplify.
[inputs]: Reformat.
 2023-04-25 19:46:29 +02:00
Ricardo Wurmus
fc80efe1a0
gnu: bedtools-2.18: Fix build. 
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Fix operators in
'compatibility phase.
 2023-04-25 19:41:05 +02:00
Ricardo Wurmus
f2e90d6f43
gnu: hisat: Build with GCC 10. 
* gnu/packages/bioinformatics.scm (hisat)[native-inputs]: Add gcc-10.
 2023-04-25 19:30:43 +02:00
Ricardo Wurmus
0a4fa99b39
gnu: kallisto: Update to 0.48.0. 
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.48.0.
[arguments]: Remove trailing #T from build phase.
 2023-04-25 19:28:42 +02:00
Ricardo Wurmus
7ae5325bf1
gnu: bpp-core: Build with GCC 10. 
* gnu/packages/bioinformatics.scm (bpp-core)[native-inputs]: Add gcc-10.
 2023-04-25 19:12:57 +02:00
Ricardo Wurmus
2c09cc19e6
gnu: vcflib: Update to 1.0.9. 
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.9.
[source]: Update snippet.
[inputs]: Add curl, pybind11, and wfa2-lib.
[arguments]: Adjust and reformat.
 2023-04-25 19:10:19 +02:00
Ricardo Wurmus
4ad51f5914
gnu: tabixpp: Update to 1.1.2. 
* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.2.
[source]: Simplify snippet.
[inputs]: Add curl.
[arguments]: Simplify and reformat.
 2023-04-25 19:10:19 +02:00
Ricardo Wurmus
8664c6230e
gnu: Add wfa2-lib. 
* gnu/packages/bioinformatics.scm (wfa2-lib): New variable.
 2023-04-25 19:10:18 +02:00
Ricardo Wurmus
3a37e3ecd8
gnu: lofreq: Set file timestamps to 1980s. 
This keeps Python from complaining: "ZIP does not support timestamps before
1980".

* gnu/packages/bioinformatics.scm (lofreq)[arguments]: Add build phase
'set-source-file-times-to-1980.
 2023-04-25 16:17:49 +02:00
Ricardo Wurmus
0ad4a4d155
gnu: lofreq: Drop input labels. 
* gnu/packages/bioinformatics.scm (lofreq)[inputs]: Drop package labels.
 2023-04-25 16:17:49 +02:00
Ricardo Wurmus
1fca85cd88
gnu: ivar: Update to 1.4.2. 
* gnu/packages/bioinformatics.scm (ivar): Update to 1.4.2.
[arguments]: Remove -Werror flag.
 2023-04-25 16:17:49 +02:00
Ricardo Wurmus
bca1496f72
gnu: multiqc: Update to 1.14. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.14.
[build-system]: Use pyproject-build-system.
[arguments]: Simplify check phase; restore sanity-check phase.
[propagated-inputs]: Add python-rich-click.
[native-inputs]: Update test data.
 2023-04-24 19:49:04 +02:00
Ricardo Wurmus
9703ecc47b
gnu: macs: Patch version check for Python. 
* gnu/packages/bioinformatics.scm (macs)[source]: Patch check for Python >
3.6.
 2023-04-24 19:49:04 +02:00
Ricardo Wurmus
913668e879
gnu: salmon: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (salmon): Update to 1.10.1.
[inputs]: Replace cereal-1.3.0 with cereal; add htscodecs.
[native-inputs]: Update hash of pufferfish sources.
 2023-04-24 19:49:04 +02:00
Ricardo Wurmus
b8a0a10308
gnu: Add htscodecs. 
* gnu/packages/bioinformatics.scm (htscodecs): New variable.
 2023-04-24 19:49:04 +02:00
Andreas Enge
d1252b597d
Merge remote-tracking branch 'origin/master' into core-updates 2023-04-22 09:21:22 +02:00
Mădălin Ionel Patrașcu
184658e282
gnu: bppsuite: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (bppsuite): Update to 2.4.1.
[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build.
[inputs]: Use list.
[home-page]: Changed to github page.
 2023-04-21 14:01:25 +02:00
Mădălin Ionel Patrașcu
2a20acf24b
gnu: bpp-popgen: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (bpp-popgen): Update to 2.4.1.
[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
 2023-04-21 14:01:22 +02:00
Mădălin Ionel Patrașcu
2babf3d7d7
gnu: Add maffilter. 
* gnu/packages/bioinformatics.scm (maffilter): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2023-04-21 13:15:02 +02:00
Mădălin Ionel Patrașcu
7c75228c8b
gnu: Add bpp-phyl-omics. 
* gnu/packages/bioinformatics.scm (bpp-phyl-omics): New variable.
 2023-04-21 12:56:39 +02:00
Mădălin Ionel Patrașcu
722a8b2296
gnu: Add bpp-seq-omics. 
* gnu/packages/bioinformatics.scm (bpp-seq-omics): New variable.
 2023-04-21 12:56:39 +02:00
Mădălin Ionel Patrașcu
5107a8a1a3
gnu: bpp-phyl: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (bpp-phyl): Update to 2.4.1.

[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build and out-of-source.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
[synopsis]: Use proper capitalization.
 2023-04-21 12:56:39 +02:00
Mădălin Ionel Patrașcu
627049872b
gnu: bpp-seq: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (bpp-seq): Update to 2.4.1.

[source]: Remove the commit and use the release version. Changed to the github
repo.
[arguments]: Remove the disabled parallel-build and out-of-source.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
 2023-04-21 12:56:38 +02:00
Mădălin Ionel Patrașcu
51ef858c94
gnu: bpp-core: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (bpp-core): Update to 2.4.1.

[source]: Remove the commit and use the release version. Changed to the github
stored sources.
[arguments]: Remove the disabled parallel-build.
[home-page]: Changed to new host Université Claude-Bernard Lyon 1.
 2023-04-21 12:56:38 +02:00
Andreas Enge
216d7bdb73
Merge remote-tracking branch 'origin/master' into core-updates 2023-04-17 19:17:39 +02:00
Navid Afkhami
b95cd3f969
gnu: Add r-demuxmix. 
* gnu/packages/bioinformatics.scm (r-demuxmix): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-04-17 11:16:30 +02:00
Navid Afkhami
2b2068a083
gnu: Add r-demultiplex2. 
* gnu/packages/bioinformatics.scm (r-demultiplex2): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-04-17 11:14:30 +02:00
Maxim Cournoyer
3bacd3c76a
Merge branch 'master' into core-updates. 
Conflicts:
	gnu/local.mk
	gnu/packages/build-tools.scm
	gnu/packages/certs.scm
	gnu/packages/check.scm
	gnu/packages/compression.scm
	gnu/packages/cups.scm
	gnu/packages/fontutils.scm
	gnu/packages/gnuzilla.scm
	gnu/packages/guile.scm
	gnu/packages/ibus.scm
	gnu/packages/image-processing.scm
	gnu/packages/linux.scm
	gnu/packages/music.scm
	gnu/packages/nss.scm
	gnu/packages/pdf.scm
	gnu/packages/python-xyz.scm
	gnu/packages/qt.scm
	gnu/packages/ruby.scm
	gnu/packages/shells.scm
	gnu/packages/tex.scm
	gnu/packages/video.scm
	gnu/packages/vulkan.scm
	gnu/packages/web.scm
	gnu/packages/webkit.scm
	gnu/packages/wm.scm
 2023-04-14 17:15:08 -04:00
Bruno Victal
acdb42e5d0
gnu: Purge pre-1.3.0 deprecated packages. 
* gnu/packages/bioinformatics.scm (deeptools): Remove variable.
* gnu/packages/efi.scm (efi_analyzer): Ditto.
* gnu/packages/guile.scm (guile-2.2/bug-fix, guile-json): Ditto.
* gnu/packages/image.scm (libjpeg): Ditto.
* gnu/packages/kde.scm (kdevplatform): Ditto
* gnu/packages/linphone.scm (linphoneqt): Ditto.
* gnu/packages/maths.scm (blis-sandybridge, blis-haswell, blis-knl): Ditto.
* gnu/packages/mpi.scm (hwloc-2.0): Ditto.
* gnu/packages/music.scm (python-abjad, zlfo): Ditto.
* gnu/packages/perl.scm (perl-base, perl-parent): Ditto.
* gnu/packages/tryton.scm (python-trytond): Ditto.
* gnu/packages/video.scm (gnome-mpv): Ditto.
* tests/graph.scm: Use guile-json-1.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-04-07 17:53:37 +02:00
Ricardo Wurmus
caf163536a
gnu: Add r-maxprobes. 
* gnu/packages/bioinformatics.scm (r-maxprobes): New variable.
 2023-03-30 14:40:01 +02:00
Ricardo Wurmus
033955b4e8
gnu: Add r-illuminahumanmethylationepicanno-ilm10b5-hg38. 
* gnu/packages/bioinformatics.scm
(r-illuminahumanmethylationepicanno-ilm10b5-hg38): New variable.
 2023-03-30 14:38:45 +02:00
Ricardo Wurmus
3f1617da19
gnu: Add r-cytoexplorer. 
* gnu/packages/bioinformatics.scm (r-cytoexplorer): New variable.
 2023-03-30 13:03:30 +02:00
Andreas Enge
ccb62d8feb
Merge remote-tracking branch 'origin/master' into core-updates 2023-03-20 18:49:06 +01:00
Ricardo Wurmus
5dcbe80da8
gnu: Add transanno. 
* gnu/packages/bioinformatics.scm (transanno): New variable.
 2023-03-20 17:22:33 +01:00
Ricardo Wurmus
4496ff34a3
gnu: Add r-conqur. 
* gnu/packages/bioinformatics.scm (r-conqur): New variable.
 2023-03-15 18:31:23 +01:00
Ricardo Wurmus
d37b467631
gnu: r-rhandsontable: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-rhandsontable): Move this variable from
here...
* gnu/packages/cran.scm (r-rhandsontable): ...to here.
 2023-03-14 17:58:28 +01:00
Navid Afkhami
204c51cac4
gnu: Add r-premessa. 
* gnu/packages/bioinformatics.scm (r-premessa): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
 2023-03-14 17:58:28 +01:00
Ricardo Wurmus
27c8ab4bf3
gnu: Add r-rhandsontable. 
* gnu/packages/bioinformatics.scm (r-rhandsontable): New variable.

Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
 2023-03-14 17:48:14 +01:00
Antero Mejr
72b1fe77b2
gnu: scvelo: Remove python-pre-commit. 
* gnu/packages/bioinformatics.scm (scvelo)[native-inputs]: Remove
python-pre-commit.

Signed-off-by: Lars-Dominik Braun <lars@6xq.net>
 2023-03-12 11:04:06 +01:00
Antero Mejr
ed59796de5
gnu: python-doubletdetection: Remove python-pre-commit. 
* gnu/packages/bioinformatics.scm (python-doubletdetection)[native-inputs]:
Remove python-pre-commit.

Signed-off-by: Lars-Dominik Braun <lars@6xq.net>
 2023-03-12 11:04:06 +01:00
Ricardo Wurmus
fe9bcf9db2
gnu: Add r-plsdabatch. 
* gnu/packages/bioinformatics.scm (r-plsdabatch): New variable.
 2023-03-06 14:55:06 +01:00
Christopher Baines
7df09ee0ab
Merge remote-tracking branch 'savannah/master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/autotools.scm
	gnu/packages/cmake.scm
	gnu/packages/gnuzilla.scm
	gnu/packages/haskell.scm
	gnu/packages/pdf.scm
	gnu/packages/python-xyz.scm
	gnu/packages/samba.scm
	gnu/packages/tex.scm
	gnu/packages/tls.scm
	gnu/packages/wxwidgets.scm
 2023-03-02 10:55:08 +00:00
Mădălin Ionel Patrașcu
60652a8efa
gnu: Add r-p2data. 
* gnu/packages/bioinformatics.scm (r-p2data): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2023-03-01 14:07:58 +01:00
Mădălin Ionel Patrașcu
df74c74688
gnu: Add r-conospanel. 
* gnu/packages/bioinformatics.scm (r-conospanel): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2023-03-01 14:06:04 +01:00
Navid Afkhami
8f084b2c7c
gnu: r-doubletcollection: Add missing inputs. 
If these Python packages are not available at runtime the package tries to
install them automatically via Conda.

* gnu/packages/bioinformatics.scm (r-doubletcollection)[propagated-inputs]:
Add python, python-scrublet, and python-doubletdetection.
 2023-03-03 23:49:14 +01:00
Navid Afkhami
c6480edbe3
gnu: Add r-seurat-utils. 
* gnu/packages/bioinformatics.scm (r-seurat-utils): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
9aad3dfd7b
gnu: Add r-tictoc. 
* gnu/packages/bioinformatics.scm (r-tictoc): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
573b65f51e
gnu: Add r-ggexpress. 
* gnu/packages/bioinformatics.scm (r-ggexpress): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
fd099793c8
gnu: Add r-markdownreports. 
* gnu/packages/bioinformatics.scm (r-markdownreports): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
8eb8af7e30
gnu: Add r-markdownhelpers. 
* gnu/packages/bioinformatics.scm (r-markdownhelpers): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
ba47b0fceb
gnu: Add r-codeandroll2. 
* gnu/packages/bioinformatics.scm (r-codeandroll2): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
877e2e7cf3
gnu: Add r-readwriter. 
* gnu/packages/bioinformatics.scm (r-readwriter): New variable.
 2023-03-03 15:11:43 +01:00
Navid Afkhami
351de7426c
gnu: Add r-stringendo. 
* gnu/packages/bioinformatics.scm (r-stringendo): New variable.
 2023-03-03 15:11:42 +01:00
Lars-Dominik Braun
baf9e0a336
gnu: ngless: Drop Haskell libraries and documentation. 
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Add
'remove-libraries phase and disable #:haddock?.
 2023-02-26 10:26:16 +01:00
Lars-Dominik Braun
49a320aaa6
Upgrade Haskell packages. 
Script-aided bulk change.
 2023-02-26 10:26:07 +01:00
Tobias Geerinckx-Rice
1e6ddceb83
gnu: Use HTTPS package home pages wherever possible. 
* gnu/packages/accessibility.scm (florence)[home-page]: Use HTTPS.
* gnu/packages/admin.scm (netcat, nmon)[home-page]: Likewise.
* gnu/packages/algebra.scm (mpfrcx, cm, flint, fftw, r-dtt)[home-page]:
Likewise.
* gnu/packages/apr.scm (apr, apr-util)[home-page]: Likewise.
* gnu/packages/aspell.scm (aspell-dict-it)[home-page]: Likewise.
* gnu/packages/astronomy.scm (casacore, sextractor, libnova)
(xplanet)[home-page]: Likewise.
* gnu/packages/audio.scm (libtimidity, alsa-modular-synth, azr3, tao)
(freepats, rakarrack, liblo, libshout-idjc, timidity++, libsbsms)
(libmodplug, libxmp, xmp, sox, drc, gsm, gnaural)
(streamripper)[home-page]: Likewise.
* gnu/packages/authentication.scm (pamtester)[home-page]: Likewise.
* gnu/packages/backup.scm (grsync)[home-page]: Likewise.
* gnu/packages/bioconductor.scm (r-nmf, r-edger, r-limma)
(r-plgem)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (python-biom-format, bowtie, bowtie1)
(bwa, crossmap, java-htsjdk, java-htsjdk-latest, java-picard)
(java-picard-2.10.3, kaiju, proteinortho, rsem, rseqc, seek, samtools)
(snap-aligner, subread, stringtie, r-centipede, prinseq, emboss, phylip)
(libsbml)[home-page]: Likewise.
* gnu/packages/build-tools.scm (tup)[home-page]: Likewise.
* gnu/packages/cdrom.scm (libcddb, cdrdao, cdrtools)
(cd-discid)[home-page]: Likewise.
* gnu/packages/check.scm (cunit, python-nose)
(python-pyhamcrest)[home-page]: Likewise.
* gnu/packages/chemistry.scm (gromacs)[home-page]: Likewise.
* gnu/packages/chez.scm (chez-fmt)[home-page]: Likewise.
* gnu/packages/code.scm (lcov, uncrustify, cscope)[home-page]: Likewise.
* gnu/packages/compression.scm (p7zip)[home-page]: Likewise.
* gnu/packages/cran.scm (r-emdist, r-proj4, r-zoo, r-ggalluvial)
(r-orgmassspecr, r-polychrome, r-partykit, r-rcpp, r-ff, r-emdbook)
(r-fitdistrplus, r-linprog, r-geometry, r-dtw, r-fst, r-rjags)
(r-intergraph, r-qualv, r-labelled, r-survey, r-coin, r-fmsb, r-tm)
(r-corpcor, r-rmpfr, r-spatialextremes, r-longitudinal, r-genenet)
(r-bayesm, r-seqinr, r-mpm, r-text2vec, r-rgdal, r-seewave, r-hdrcde)
(r-shapes, r-anytime, r-stm, r-d3network, r-tam, r-directlabels)
(r-spatstat-utils, r-spatstat-sparse, r-spatstat-data, r-spatstat-geom)
(r-spatstat-core, r-spatstat-linnet, r-spatstat-random, r-spatstat)
(r-rcpptoml, r-mlecens, r-seurat, r-mlearning, r-zooimage)[home-page]:
Likewise.
* gnu/packages/crates-io.scm (rust-nickel-0.11, rust-thrift-0.13)
(rust-trust-dns-https-0.20, rust-trust-dns-native-tls-0.20)
(rust-trust-dns-openssl-0.20, rust-trust-dns-proto-0.20)
(rust-trust-dns-resolver-0.20, rust-trust-dns-rustls-0.20)
(rust-uint-0.9, rust-yaml-rust-0.4)[home-page]: Likewise.
* gnu/packages/crypto.scm (libdecaf, ccrypt)[home-page]: Likewise.
* gnu/packages/curl.scm (curlpp)[home-page]: Likewise.
* gnu/packages/databases.scm (python-pylibmc, unixodbc, wiredtiger)
(libpqxx, mdbtools, virtuoso-ose, libdbi, libdbi-drivers)
(soci)[home-page]: Likewise.
* gnu/packages/debian.scm (apt-mirror)[home-page]: Likewise.
* gnu/packages/debug.scm (remake)[home-page]: Likewise.
* gnu/packages/disk.scm (sdparm, idle3-tools, duc)[home-page]: Likewise.
* gnu/packages/django.scm (python-django-haystack)[home-page]: Likewise.
* gnu/packages/djvu.scm (djvulibre, djview)[home-page]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[home-page]: Likewise.
* gnu/packages/docbook.scm (dblatex, docbook2x)[home-page]: Likewise.
* gnu/packages/documentation.scm (scrollkeeper)[home-page]: Likewise.
* gnu/packages/ebook.scm (liblinebreak)[home-page]: Likewise.
* gnu/packages/electronics.scm (xoscope)[home-page]: Likewise.
* gnu/packages/emacs-xyz.scm (emacs-bbdb, emacs-caps-lock, emacs-djvu)
(emacs-pabbrev, emacs-twittering-mode, emacs-filladapt, emacs-rudel)
(emacs-stream, emacspeak, emacs-cc-mode, emacs-eldoc, emacs-jsonrpc)
(emacs-gtk-look, emacs-xclip, emacs-slime-volleyball, emacs-minimap)
(emacs-auto-dictionary-mode, emacs-persist, emacs-shell-command+)
(emacs-map, emacs-xref, emacs-dictionary)[home-page]: Likewise.
* gnu/packages/embedded.scm (sdcc)[home-page]: Likewise.
* gnu/packages/engineering.scm (asco, libngspice, libspnav)
(openctm)[home-page]: Likewise.
* gnu/packages/erlang.scm (erlang-erlware-commons)[home-page]: Likewise.
* gnu/packages/file-systems.scm (jfsutils, curlftpfs)[home-page]:
Likewise.
* gnu/packages/finance.scm (gbonds)[home-page]: Likewise.
* gnu/packages/flashing-tools.scm (dfu-util, srecord)[home-page]:
Likewise.
* gnu/packages/fltk.scm (ntk)[home-page]: Likewise.
* gnu/packages/fonts.scm (font-terminus, font-tex-gyre)
(font-comic-neue)[home-page]: Likewise.
* gnu/packages/fontutils.scm (ttf2pt1, potrace, libspiro)[home-page]:
Likewise.
* gnu/packages/fpga.scm (icestorm, gtkwave, gtkwave)
(python-myhdl)[home-page]: Likewise.
* gnu/packages/freedesktop.scm (libatasmart)[home-page]: Likewise.
* gnu/packages/ftp.scm (weex)[home-page]: Likewise.
* gnu/packages/game-development.scm (dds, python-tmx, sfxr, quesoglc)
(eureka, plib)[home-page]: Likewise.
* gnu/packages/games.scm (abe, alex4, armagetronad, barony)
(foobillard++, golly, ltris, pipewalker, prboom-plus, trigger-rally)
(cmatrix, pinball, pioneers, tennix, chromium-bsu, freeciv, kiki)
(quakespasm, frotz, frotz-dumb-terminal, frotz-sdl, btanks)
(flare-engine, chessx, barrage, cgoban, passage)[home-page]: Likewise.
* gnu/packages/geo.scm (python-geopandas, saga)[home-page]: Likewise.
* gnu/packages/gl.scm (freeglut, gl2ps)[home-page]: Likewise.
* gnu/packages/gnome.scm (cogl, clutter-gtk, clutter-gst, bluefish)
(workrave)[home-page]: Likewise.
* gnu/packages/gnustep.scm (wmnd, wmfire, wmfire)[home-page]: Likewise.
* gnu/packages/graph.scm (mscgen)[home-page]: Likewise.
* gnu/packages/graphics.scm (assimp, alembic, ctl, agg)
(opencsg)[home-page]: Likewise.
* gnu/packages/graphviz.scm (gts)[home-page]: Likewise.
* gnu/packages/gtk.scm (gtkspell3)[home-page]: Likewise.
* gnu/packages/guile-xyz.scm (guile-irregex)[home-page]: Likewise.
* gnu/packages/haskell-apps.scm (cpphs)[home-page]: Likewise.
* gnu/packages/haskell-check.scm (ghc-hunit)[home-page]: Likewise.
* gnu/packages/haskell-web.scm (ghc-http-client-restricted)
(ghc-blaze-html, ghc-happstack-server, ghc-sourcemap)[home-page]:
Likewise.
* gnu/packages/haskell-xyz.scm (ghc-assoc, ghc-cairo, ghc-cborg)
(ghc-csv, ghc-glob, ghc-gtk2hs-buildtools, ghc-hmatrix-gsl-stats)
(ghc-intervalmap, ghc-lens-family-core, ghc-managed, ghc-mountpoints)
(ghc-network-multicast, ghc-optional-args, ghc-regex, ghc-spoon)
(ghc-transformers, ghc-turtle, ghc-utf8-light, ghc-wizards)
(ghc-template-haskell, ghc-boot-th, ghc-binary-orphans)
(ghc-postgresql-simple)[home-page]: Likewise.
* gnu/packages/hexedit.scm (ht, bvi)[home-page]: Likewise.
* gnu/packages/hunspell.scm (hunspell-dict-hu)[home-page]: Likewise.
* gnu/packages/image-processing.scm (mia)[home-page]: Likewise.
* gnu/packages/image-viewers.scm (geeqie, gpicview, luminance-hdr)
(qiv)[home-page]: Likewise.
* gnu/packages/image.scm (libuemf, devil, steghide, optipng, niftilib)
(sng, mtpaint)[home-page]: Likewise.
* gnu/packages/java-xml.scm (java-simple-xml, java-jaxp)
(java-apache-xml-commons-resolver)[home-page]: Likewise.
* gnu/packages/java.scm (java-cisd-base, java-cisd-args4j)
(java-hamcrest-core, java-jsr305, java-eclipse-osgi)
(java-eclipse-equinox-common, java-eclipse-core-jobs)
(java-eclipse-equinox-registry, java-eclipse-equinox-app)
(java-eclipse-equinox-preferences, java-eclipse-core-contenttype)
(java-eclipse-text, java-treelayout, java-aopalliance, java-jeromq)
(java-cdi-api)[home-page]: Likewise.
* gnu/packages/jemalloc.scm (jemalloc-4.5.0)[home-page]: Likewise.
* gnu/packages/julia-xyz.scm (julia-recipespipeline)[home-page]:
Likewise.
* gnu/packages/kde-internet.scm (kget)[home-page]: Likewise.
* gnu/packages/kde-systemtools.scm (dolphin-plugins)
(konsole)[home-page]: Likewise.
* gnu/packages/kodi.scm (fstrcmp)[home-page]: Likewise.
* gnu/packages/language.scm (hime, libchewing)[home-page]: Likewise.
* gnu/packages/lego.scm (nqc)[home-page]: Likewise.
* gnu/packages/lesstif.scm (lesstif)[home-page]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[home-page]: Likewise.
* gnu/packages/libdaemon.scm (libdaemon)[home-page]: Likewise.
* gnu/packages/libffi.scm (libffi)[home-page]: Likewise.
* gnu/packages/libreoffice.scm (libwpd, libwpg, libwps)[home-page]:
Likewise.
* gnu/packages/libusb.scm (libmtp, gmtp)[home-page]: Likewise.
* gnu/packages/linux.scm (e2fsprogs, extundelete, lsscsi, net-tools)
(kbd, sysfsutils, cpuid, libpfm4)[home-page]: Likewise.
* gnu/packages/lisp-check.scm (sbcl-ptester, sbcl-xlunit)[home-page]:
Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-html-encode, sbcl-py-configparser)
(sbcl-cl-utilities, sbcl-series, sbcl-uffi, sbcl-clsql, sbcl-sycamore)
(sbcl-osicat, sbcl-hu.dwim.common, sbcl-caveman, sbcl-trivial-shell)
(sbcl-trivial-benchmark, sbcl-screamer, sbcl-smug)[home-page]: Likewise.
* gnu/packages/lisp.scm (lush2)[home-page]: Likewise.
* gnu/packages/logging.scm (log4cpp)[home-page]: Likewise.
* gnu/packages/lua.scm (lua-ldoc)[home-page]: Likewise.
* gnu/packages/machine-learning.scm (mcl, openfst, rxcpp)[home-page]:
Likewise.
* gnu/packages/mail.scm (muchsync, procmail, sendmail)
(opensmtpd-filter-dkimsign, crm114)[home-page]: Likewise.
* gnu/packages/man.scm (libpipeline, man-db)[home-page]: Likewise.
* gnu/packages/maths.scm (lapack, scalapack, hdf-eos5, itpp, gmsh)
(metamath, p4est, armadillo, suitesparse, atlas, lpsolve, wcalc, why3)
(frama-c)[home-page]: Likewise.
* gnu/packages/mcrypt.scm (mcrypt, libmcrypt, libmhash)[home-page]:
Likewise.
* gnu/packages/minetest.scm (minetest-advtrains)[home-page]: Likewise.
* gnu/packages/monitoring.scm (python-whisper, python-carbon)
(hostscope)[home-page]: Likewise.
* gnu/packages/mp3.scm (id3lib, libmp3splt, mp3splt, mpg321)
(lame)[home-page]: Likewise.
* gnu/packages/multiprecision.scm (mpc)[home-page]: Likewise.
* gnu/packages/music.scm (aria-maestosa, lingot, setbfree, bristol)
(portmidi, python-pyportmidi, zynaddsubfx, yoshimi, aj-snapshot)
(schismtracker, midicsv, midicsv, qmidiarp, qmidiroute, dssi, tap-lv2)
(shiru-lv2)[home-page]: Likewise.
* gnu/packages/ncurses.scm (stfl)[home-page]: Likewise.
* gnu/packages/networking.scm (lksctp-tools, mbuffer, ifstatus, bird)
(tunctl, traceroute)[home-page]: Likewise.
* gnu/packages/node-xyz.scm (node-mersenne)[home-page]: Likewise.
* gnu/packages/ntp.scm (openntpd)[home-page]: Likewise.
* gnu/packages/ocaml.scm (opam, hevea, ocaml-menhir, ocaml-piqilib)
(ocaml-graph, cubicle)[home-page]: Likewise.
* gnu/packages/opencl.scm (python-pyopencl)[home-page]: Likewise.
* gnu/packages/package-management.scm (xstow, modules)[home-page]:
Likewise.
* gnu/packages/parallel.scm (xjobs)[home-page]: Likewise.
* gnu/packages/pdf.scm (podofo, qpdf, xournal, impressive)[home-page]:
Likewise.
* gnu/packages/perl.scm (perl-math-vecstat, perltidy)[home-page]:
Likewise.
* gnu/packages/photo.scm (libpano13, enblend-enfuse, hugin)[home-page]:
Likewise.
* gnu/packages/plan9.scm (drawterm)[home-page]: Likewise.
* gnu/packages/plotutils.scm (guile-charting, ploticus)[home-page]:
Likewise.
* gnu/packages/popt.scm (argtable, popt)[home-page]: Likewise.
* gnu/packages/profiling.scm (otf2)[home-page]: Likewise.
* gnu/packages/pulseaudio.scm (pulseaudio)[home-page]: Likewise.
* gnu/packages/python-check.scm (python-mypy)[home-page]: Likewise.
* gnu/packages/python-web.scm (python-cssutils)
(python-translationstring)[home-page]: Likewise.
* gnu/packages/python-xyz.scm (python-diskcache, python-doxyqml)
(python-docutils, python-pexpect, python-importlib-resources)
(python-simplegeneric, python-urwid, python-xlrd, python-xlwt)
(python-pyasn1, python-pythondialog, python-tftpy, python-random2)
(python-arcp, python-pyopengl, python-sortedcollections)
(python-sortedcontainers, python-yapsy, python-pydispatcher)
(python-posix-ipc)[home-page]: Likewise.
* gnu/packages/qt.scm (qwt, libqglviewer, signond)[home-page]: Likewise.
* gnu/packages/radio.scm (unixcw, gnuais)[home-page]: Likewise.
* gnu/packages/raspberry-pi.scm (bcm2835)[home-page]: Likewise.
* gnu/packages/rdf.scm (clucene, rasqal, redland)[home-page]: Likewise.
* gnu/packages/regex.scm (tre)[home-page]: Likewise.
* gnu/packages/rsync.scm (librsync)[home-page]: Likewise.
* gnu/packages/ruby.scm (ruby-packnga, ruby-nokogiri, ruby-oj, ruby-ox)
(ruby-sinatra, ruby-citrus, ruby-cbor, ruby-roda)[home-page]: Likewise.
* gnu/packages/scheme.scm (scheme48, tinyscheme)[home-page]: Likewise.
* gnu/packages/screen.scm (dtach)[home-page]: Likewise.
* gnu/packages/scsi.scm (sg3-utils)[home-page]: Likewise.
* gnu/packages/sdl.scm (libmikmod, sdl-pango)[home-page]: Likewise.
* gnu/packages/shellutils.scm (hstr, rig)[home-page]: Likewise.
* gnu/packages/simulation.scm (python-dolfin-adjoint)[home-page]:
Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[home-page]: Likewise.
* gnu/packages/speech.scm (espeak)[home-page]: Likewise.
* gnu/packages/stalonetray.scm (stalonetray)[home-page]: Likewise.
* gnu/packages/statistics.scm (jags, r-mass, r-class, r-lattice)
(r-matrix, r-nnet, r-spatial, r-bit, r-bit64, r-digest, r-xtable)
(python-statsmodels, r-ade4, r-latticeextra, r-rcurl, r-xml, r-mvtnorm)
(r-robustbase, r-minqa, r-fdrtool, java-jdistlib, xlispstat)[home-page]:
Likewise.
* gnu/packages/swig.scm (swig)[home-page]: Likewise.
* gnu/packages/task-management.scm (wtime)[home-page]: Likewise.
* gnu/packages/tcl.scm (itcl, tclxml, tclx)[home-page]: Likewise.
* gnu/packages/terminals.scm (libtermkey, mlterm, libvterm)
(libvterm)[home-page]: Likewise.
* gnu/packages/tex.scm (texlive-lm, texlive-lm-math, texlive-cs)
(texlive-csplain, biber, texmaker)[home-page]: Likewise.
* gnu/packages/text-editors.scm (joe)[home-page]: Likewise.
* gnu/packages/textutils.scm (drm-tools, docx2txt)[home-page]: Likewise.
* gnu/packages/tv.scm (tvtime)[home-page]: Likewise.
* gnu/packages/unicode.scm (libunibreak)[home-page]: Likewise.
* gnu/packages/upnp.scm (libupnp)[home-page]: Likewise.
* gnu/packages/version-control.scm (cvs)[home-page]: Likewise.
* gnu/packages/video.scm (transcode, libquicktime, mjpegtools, aalib)
(liba52, libmpeg2, x265, libdv, dvdauthor, aegisub, pitivi, gavl)
(dvdbackup, guvcview, video-contact-sheet)[home-page]: Likewise.
* gnu/packages/virtualization.scm (bochs)[home-page]: Likewise.
* gnu/packages/w3m.scm (w3m)[home-page]: Likewise.
* gnu/packages/web.scm (qjson, libquvi-scripts, libquvi, quvi)
(tidy-html, htmlcxx)[home-page]: Likewise.
* gnu/packages/wm.scm (evilwm, menumaker)[home-page]: Likewise.
* gnu/packages/wv.scm (wv)[home-page]: Likewise.
* gnu/packages/wxwidgets.scm (wxsvg)[home-page]: Likewise.
* gnu/packages/xdisorg.scm (mtdev, xsel)[home-page]: Likewise.
* gnu/packages/xfig.scm (xfig, transfig)[home-page]: Likewise.
* gnu/packages/xml.scm (openjade, python-pyxb, xmlstarlet, xmlrpc-c)
(opensp)[home-page]: Likewise.
* gnu/packages/xorg.scm (xf86-video-qxl)[home-page]: Likewise.
 2023-02-19 01:00:01 +01:00
Efraim Flashner
672036c6df
gnu: Remove unneeded module imports. 
* gnu/packages/abiword.scm,
* gnu/packages/ada.scm,
* gnu/packages/agda.scm,
* gnu/packages/backup.scm,
* gnu/packages/barrier.scm,
* gnu/packages/bioinformatics.scm,
* gnu/packages/bootstrap.scm,
* gnu/packages/bqn.scm,
* gnu/packages/c.scm,
* gnu/packages/chemistry.scm,
* gnu/packages/coq.scm,
* gnu/packages/cross-base.scm,
* gnu/packages/databases.scm,
* gnu/packages/emacs-xyz.scm,
* gnu/packages/enlightenment.scm,
* gnu/packages/games.scm,
* gnu/packages/geo.scm,
* gnu/packages/ghostscript.scm,
* gnu/packages/gl.scm,
* gnu/packages/golang.scm,
* gnu/packages/jami.scm,
* gnu/packages/java-maths.scm,
* gnu/packages/kde-frameworks.scm,
* gnu/packages/kde-plasma.scm,
* gnu/packages/language.scm,
* gnu/packages/libreoffice.scm,
* gnu/packages/linphone.scm,
* gnu/packages/lisp.scm,
* gnu/packages/llvm.scm,
* gnu/packages/machine-learning.scm,
* gnu/packages/minetest.scm,
* gnu/packages/monitoring.scm,
* gnu/packages/nfs.scm,
* gnu/packages/ocr.scm,
* gnu/packages/opencl.scm,
* gnu/packages/pdf.scm,
* gnu/packages/python-xyz.scm,
* gnu/packages/racket.scm,
* gnu/packages/rust.scm,
* gnu/packages/syncthing.scm,
* gnu/packages/syndication.scm,
* gnu/packages/telegram.scm,
* gnu/packages/vulkan.scm,
* gnu/packages/web-browsers.scm,
* gnu/packages/web.scm,
* gnu/packages/webkit.scm: Remove some unecessary module imports.
 2023-02-16 22:41:03 +02:00
Ricardo Wurmus
b6a4fbb488
gnu: fastqc: Update to 0.11.9. 
* gnu/packages/bioinformatics.scm (fastqc): Update to 0.11.9.
[source]: Fetch via git; delete bundled jar files.
[arguments]: Also patch .classpath file in 'fix-dependencies; fix patching of
reference to java in fastqc wrapper; override CLASSPATH.
 2023-02-16 16:56:10 +01:00
Ricardo Wurmus
67d2f688fb
gnu: jellyfish: Remove confusing quoting syntax. 
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Do not mix
quasiquote with gexp.
 2023-02-13 23:09:23 +01:00
Ricardo Wurmus
661e995c70
gnu: jellyfish: Drop input labels. 
* gnu/packages/bioinformatics.scm (jellyfish)[native-inputs]: Drop package
labels.
 2023-02-13 23:09:23 +01:00
Ricardo Wurmus
4ef9ac7f27
gnu: fastp: Update to 0.23.2. 
* gnu/packages/bioinformatics.scm (fastp): Update to 0.23.2.
[inputs]: Remove zlib; add isa-l and libdeflate.
 2023-02-13 23:09:23 +01:00
Ricardo Wurmus
54b431b7b3
gnu: fastp: Simplify. 
* gnu/packages/bioinformatics.scm (fastp)[arguments]: Simplify gexp.
 2023-02-13 23:09:23 +01:00
Ricardo Wurmus
7260cc75da
gnu: fastqc: Use gexp. 
* gnu/packages/bioinformatics.scm (fastqc)[arguments]: Use gexp; drop
trailing #T from build phase.
[inputs]: Drop package labels.
 2023-02-13 23:09:23 +01:00
Efraim Flashner
48903df6cb
gnu: go-github-com-biogo-hts-bam: Update to 1.4.4. 
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam): Update
to 1.4.4.
 2023-02-11 19:05:02 +02:00
Ricardo Wurmus
8a0b625a2d
gnu: scregseg: Update to 0.1.3. 
* gnu/packages/bioinformatics.scm (scregseg): Update to 0.1.3.
[source]: Simplify snippet.
[build-system]: Use pyproject-build-system.
[arguments]: Add phases 'set-numba-cache-dir and 'build-extensions; enable
tests.
 2023-02-10 19:41:54 +01:00
Ricardo Wurmus
fea66096a2
gnu: Add python-doubletdetection. 
* gnu/packages/bioinformatics.scm (python-doubletdetection): New variable.

Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
 2023-02-10 19:36:36 +01:00
Ricardo Wurmus
8340acfa5a
gnu: Add python-phenograph. 
* gnu/packages/bioinformatics.scm (python-phenograph): New variable.
 2023-02-10 19:36:29 +01:00
Ricardo Wurmus
769346eef7
gnu: Add louvain. 
* gnu/packages/bioinformatics.scm (louvain): New variable.
 2023-02-10 15:48:51 +01:00
Navid Afkhami
4d35a5e2b6
gnu: Add python-scrublet. 
* gnu/packages/bioinformatics.scm (python-scrublet): New variable.
 2023-02-09 11:05:29 +01:00
Navid Afkhami
532dace22d
gnu: Add bitmapperbs. 
* gnu/packages/bioinformatics.scm (bitmapperbs): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2023-02-07 19:38:44 +01:00
Ricardo Wurmus
a083a9b512
Revert "gnu: Add bitmapperbs." 
This reverts commit f55cc9cb0f.
This commit was prematurely pushed.
 2023-02-07 15:36:21 +01:00
Navid Afkhami
f55cc9cb0f
gnu: Add bitmapperbs. 
* gnu/packages/bioinformatics.scm (bitmapperbs): New variable.
 2023-02-07 15:04:12 +01:00
Ricardo Wurmus
a582d86346
gnu: Add r-ggsankey. 
* gnu/packages/bioinformatics.scm (r-ggsankey): New variable.
 2023-02-06 10:52:24 +01:00
Navid Afkhami
a60c750eec
gnu: Add r-psupertime. 
* gnu/packages/bioinformatics.scm (r-psupertime): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-02-03 16:57:00 +01:00
Navid Afkhami
59b102cab9
gnu: Add python-demuxem. 
* gnu/packages/bioinformatics.scm (python-demuxem): New variable.
 2023-02-03 11:34:42 +01:00
Navid Afkhami
89d76adf98
gnu: Add python-pegasusio. 
* gnu/packages/bioinformatics.scm (python-pegasusio): New variable.
 2023-02-03 11:34:42 +01:00
Navid Afkhami
ef879d7f40
gnu: Add r-streamgraph. 
* gnu/packages/bioinformatics.scm (r-streamgraph): New variable.
 2023-02-03 11:34:38 +01:00
Efraim Flashner
7b58f14445
gnu: texlive-fancyvrb: Use over deprecated texlive-latex-fancyvrb. 
* gnu/packages/bioinformatics.scm (phyml)[native-inputs],
* gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Replace
texlive-latex-fancyvrb with texlive-fancyvrb.
 2023-01-30 20:07:50 +02:00
Efraim Flashner
bd3e3d87a9
gnu: texlive-graphics: Use over deprecated texlive-latex-graphics. 
* gnu/packages/bioinformatics.scm (phyml)[native-inputs],
* gnu/packages/chemistry.scm (yaehmop)[native-inputs],
* gnu/packages/graphviz.scm (dot2tex)[propagated-inputs],
* gnu/packages/maths.scm (cddlib)[native-inputs],
* gnu/packages/statistics.scm (r-with-tests)[native-inputs],
* gnu/packages/tex.scm (texlive-apa6)[propagated-inputs]: Replace
texlive-latex-graphics with texlive-graphics.
 2023-01-30 20:07:49 +02:00
Efraim Flashner
4cf1acc7f3
Merge remote-tracking branch 'origin/master' into core-updates 
Conflicts:
	doc/guix.texi
	gnu/local.mk
	gnu/packages/admin.scm
	gnu/packages/base.scm
	gnu/packages/chromium.scm
	gnu/packages/compression.scm
	gnu/packages/databases.scm
	gnu/packages/diffoscope.scm
	gnu/packages/freedesktop.scm
	gnu/packages/gnome.scm
	gnu/packages/gnupg.scm
	gnu/packages/guile.scm
	gnu/packages/inkscape.scm
	gnu/packages/llvm.scm
	gnu/packages/openldap.scm
	gnu/packages/pciutils.scm
	gnu/packages/ruby.scm
	gnu/packages/samba.scm
	gnu/packages/sqlite.scm
	gnu/packages/statistics.scm
	gnu/packages/syndication.scm
	gnu/packages/tex.scm
	gnu/packages/tls.scm
	gnu/packages/version-control.scm
	gnu/packages/xml.scm
	guix/build-system/copy.scm
	guix/scripts/home.scm
 2023-01-30 12:39:40 +02:00
Tor-björn Claesson
a84ceaa8b2
gnu: gdcm: Add documentation. 
* gnu/packages/bioinformatics.scm (gdcm)[outputs]: New field.
[arguments]: Add #:phases.  Augment #:configure-flags.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-01-25 23:50:42 +01:00
Tor-björn Claesson
56551281a5
gnu: gdcm: Ignore 3 failing tests. 
* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Skip three more
failing tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-01-25 23:50:42 +01:00
Ricardo Wurmus
0d713e0140
gnu: Add python-slamdunk. 
* gnu/packages/bioinformatics.scm (python-slamdunk): New variable.
 2023-01-25 15:24:48 +01:00
Mădălin Ionel Patrașcu
718223c58c
gnu: Add python-phylophlan. 
* gnu/packages/bioinformatics.scm (python-phylophlan): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
 2023-01-25 00:22:53 +01:00
Mădălin Ionel Patrașcu
ed56d2a1c2
gnu: Add python-hclust2. 
* gnu/packages/bioinformatics.scm (python-hclust2): New variable.
 2023-01-25 00:22:53 +01:00
Mădălin Ionel Patrașcu
47839a9ed6
gnu: Add python-cmseq. 
* gnu/packages/bioinformatics.scm (python-cmseq): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
 2023-01-25 00:22:53 +01:00
Ricardo Wurmus
9558da5bb4
gnu: Add python-bcbio-gff/biopython-1.73. 
* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73): New variable.
 2023-01-25 00:22:53 +01:00
Navid Afkhami
43b7a033e3
gnu: Add r-tsis. 
* gnu/packages/bioinformatics.scm (r-tsis): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-01-20 11:06:43 +01:00
Navid Afkhami
ddfe68ebbe
gnu: Add r-doubletcollection. 
* gnu/packages/bioinformatics.scm (r-doubletcollection): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-01-20 11:02:37 +01:00
Simon Tournier
a7f1a1c0f0
gnu: Add python-vireosnp. 
* gnu/packages/bioinformatics.scm (python-vireosnp): New variable.
 2023-01-20 10:40:59 +01:00
Tobias Geerinckx-Rice
ae071e21f3
gnu: gdcm: Fix recursive Git source hash. 
The hash being used covered only the gdcm repository, not the gdcmdata
submodule.

* gnu/packages/bioinformatics.scm (gdcm)[source]: Update hash.

Reported by civodul in #guix.
 2023-01-15 01:00:00 +01:00
Tor-björn Claesson
2bdbd962e3
gnu: gdcm: Update to 3.0.20. 
* gnu/packages/bioinformatics.scm (gdcm): Update to 3.0.20.
[home-page, license]: Update.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-01-17 16:05:20 +01:00
Ricardo Wurmus
bdcdab3676
gnu: r-cytonorm: Update to 0.0.10-1.166f9ff. 
* gnu/packages/bioinformatics.scm (r-cytonorm): Update to 0.0.10-1.166f9ff.
 2023-01-16 23:54:20 +01:00
Ricardo Wurmus
9ad5c3deea
gnu: r-signac: Update to 1.9.0-1.af41427. 
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.9.0-1.af41427.
[propagated-inputs]: Remove r-ggforce, r-ggrepel, r-ggseqlogo, r-lsa,
r-qlcmatrix, and r-seurat; add r-vctrs.
 2023-01-13 10:51:23 +01:00
Marius Bakke
7f7907335d
gnu: python-cellbender: Update source hash. 
The git tag was moved in-place from d82893c05b4e6b912f7f165dc2cd7c36f29cfc52
to d92cfc5a55c8b1771348468035993c52df975170.

* gnu/packages/bioinformatics.scm (python-cellbender)[source](sha256): Update.
 2023-01-13 03:19:40 +01:00
Simon Tournier
483bc044eb
gnu: Add cellsnp-lite. 
* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable.
 2023-01-12 21:37:56 +01:00
Ricardo Wurmus
de48bcee07
gnu: Add r-gg3d. 
* gnu/packages/bioinformatics.scm (r-gg3d): New variable.
 2023-01-09 14:50:26 +01:00
Ricardo Wurmus
a4d9ce5488
gnu: Move Java XML packages to new module. 
* gnu/packages/xml.scm (java-simple-xml, java-jaxp,
java-apache-xml-commons-resolver, java-jaxen, java-xom, java-xsdlib,
java-xpp3, java-xmlpull2, java-xmlpull-api-v1, java-dom4j, java-kxml2,
java-stax, java-jettison, java-jdom2, java-xstream, java-mxparser): Move these
variables from here...
* gnu/packages/java-xml.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Register new file.
* gnu/packages/axoloti.scm,
gnu/packages/batik.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/groovy.scm,
gnu/packages/java.scm,
gnu/packages/maven.scm: Adjust module imports.
 2023-01-08 23:20:59 +01:00
Antero Mejr
15caeb745c
gnu: Add gdcm. 
* gnu/packages/bioinformatics.scm (gdcm): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-01-08 16:11:45 +01:00
Marius Bakke
edbacab995
gnu: Use old setuptools in packages that relies on use_2to3 conversion. 
This fixes a regression since 520cdf8058 where
the use_2to3 functionality was removed from setuptools.

* gnu/packages/graph.scm (python-louvain)[native-inputs]: Change from
PYTHON-SETUPTOOLS to PYTHON-SETUPTOOLS-57.
* gnu/packages/python-check.scm (python-parameterizedtestcase)[native-inputs]:
Likewise.
* gnu/packages/python-xyz.scm (python-anyjson)[native-inputs]: Add
PYTHON-SETUPTOOLS-57.
* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Change from
PYTHON-SETUPTOOLS-FOR-TENSORFLOW to PYTHON-SETUPTOOLS-57.
 2023-01-07 21:04:26 +01:00
Ricardo Wurmus
1dd8359fa2
gnu: bbmap: Update to 39.01. 
* gnu/packages/bioinformatics.scm (bbmap): Update to 39.01.
 2023-01-06 15:12:07 +01:00
Ricardo Wurmus
f72dc615ab
gnu: bbmap: Use gexp. 
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Use gexp.
 2023-01-06 15:11:48 +01:00
Ricardo Wurmus
04ea0e7de4
gnu: nanopolish: Drop input labels. 
* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Drop labels.
 2023-01-06 15:01:05 +01:00
Ricardo Wurmus
24e5dbb57a
gnu: nanopolish: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (nanopolish): Update to 0.14.0.
[source]: Update snippet.
[arguments]: Use gexp; use cc-for-target; drop #T from build phases.
[inputs]: Add minimap2.
[native-inputs]: Add cmake-minimal.
 2023-01-06 14:51:55 +01:00
Ricardo Wurmus
8ace894681
gnu: filtlong: Use Python 3. 
* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Replace python-2 with
python-wrapper.
 2023-01-06 14:06:13 +01:00
Ricardo Wurmus
067c8a7445
gnu: filtlong: Use gexp. 
* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Use gexp.
 2023-01-06 14:05:58 +01:00
Ricardo Wurmus
0070e52ade
gnu: filtlong: Drop input labels. 
* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Drop labels.
 2023-01-06 13:59:04 +01:00
Ricardo Wurmus
f5ffcd31c2
gnu: filtlong: Remove trailing #T from build phases. 
* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Remove trailing #T.
 2023-01-06 13:58:05 +01:00
Ricardo Wurmus
e20ca244db
gnu: ngless: Use gexp. 
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Use gexp.
 2023-01-06 13:56:34 +01:00
Ricardo Wurmus
648c370f33
gnu: ngless: Remove trailing #T from build phases. 
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Remove trailing #T.
 2023-01-06 13:45:06 +01:00
Ricardo Wurmus
ec5b9fe27e
gnu: bamtools: Build shared libraries. 
* gnu/packages/bioinformatics.scm (bamtools)[arguments]: Build shared
libraries instead of static libs.
 2023-01-04 19:49:59 +01:00
Ricardo Wurmus
10e1025c63
gnu: Add scallop. 
* gnu/packages/bioinformatics.scm (scallop): New variable.
 2023-01-04 17:14:01 +01:00
Ricardo Wurmus
cad1789b3e
gnu: Add python-bcbio-gff. 
* gnu/packages/bioinformatics.scm (python-bcbio-gff): New variable.
 2023-01-03 15:43:25 +01:00
Ricardo Wurmus
e84f17ea93
gnu: Add r-domultibarheatmap. 
* gnu/packages/bioinformatics.scm (r-domultibarheatmap): New variable.
 2022-12-30 15:06:12 +01:00
Ricardo Wurmus
bbada5967d
gnu: r-giotto: Update to 1.1.2-1.3c8067c. 
* gnu/packages/bioinformatics.scm (r-giotto): Update to 1.1.2-1.3c8067c.
 2022-12-28 19:26:10 +01:00
Ricardo Wurmus
d8a9d55b57
gnu: Add r-bedtorch. 
* gnu/packages/bioinformatics.scm (r-bedtorch): New variable.
 2022-12-22 11:18:02 +01:00