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Author SHA1 Message Date
Tobias Geerinckx-Rice
75b95af9d6
gnu: mash: Fix build. 
* gnu/packages/bioinformatics.scm (mash)[arguments]: Add a
new 'bootstrap phase.
 2023-07-30 02:00:00 +02:00
Tobias Geerinckx-Rice
096fd9c3ff
gnu: mash: Update package style. 
* gnu/packages/bioinformatics.scm (mash)[arguments]: Consolidate
similar SUBSTITUTE* calls.  Don't explicitly return #t from phases.
 2023-07-30 02:00:00 +02:00
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