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Author SHA1 Message Date
Efraim Flashner
b2887da40c
multiqc: Don't propagate inputs. 
* gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Move all
packages ...
[inputs]: ... to here.
 2023-09-26 13:36:02 +03:00
Mădălin Ionel Patrașcu
e134686cea
gnu: python-pygenometracks: Remove syntax error in setup.py. 
* gnu/packages/bioinformatics.scm (python-pygenometracks)[arguments]:
Add phase remove-invalid-syntax.
 2023-09-24 13:50:55 +02:00
Efraim Flashner
0792d99466
gnu: htslib: Link against htscodecs. 
* gnu/packages/bioinformatics.scm (htslib)[source]: Add snippet to
remove bundled htscodecs.
[arguments]: Add configure-flag to link against htscodecs.
[propagated-inputs]: Add htscodecs.
(htslib-1.14, htslib-1.12): Use bundled htscodecs.
 2023-09-24 11:15:17 +03:00
Efraim Flashner
a338a553e3
gnu: htscodecs: Update to 1.5.1. 
* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.5.1.
 2023-09-24 10:53:07 +03:00
Efraim Flashner
f45c0c8228
gnu: wfa2-lib: Mark package as tunable. 
* gnu/packages/bioinformatics.scm (wfa2-lib)[properties]: New field.
 2023-09-22 09:32:11 +03:00
Marius Bakke
fdfafaa48c
gnu: python-bwapy: Fix typo. 
* gnu/packages/bioinformatics.scm (python-bwapy)[synopsis]: Fix typo.
 2023-09-22 01:29:21 +08:00
Marius Bakke
86d1f12363
gnu: python-arboreto: Add missing inputs. 
* gnu/packages/bioinformatics.scm (python-arboreto)[propagated-inputs]: Add
PYTHON-LZ4 and PYTHON-PYARROW.
 2023-09-22 01:29:21 +08:00
Efraim Flashner
7a2ee8524a
gnu: wfmash: Update to 0.10.5. 
* gnu/packages/bioinformatics.scm (wfmash): Update to 0.10.5.
[source]: Update to changes in source code.
[arguments]: Add configure-flag to enable more features.
[native-inputs]: Add pkg-config.
 2023-09-20 09:53:52 +03:00
Mădălin Ionel Patrașcu
1c8e159335
gnu: python-plastid: Patch it for python 3.10. 
* gnu/packages/bioinformatics.scm (python-plastid)[arguments]: Add new phase
'patch-for-python-3.10.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-09-18 10:25:26 +02:00
Ricardo Wurmus
c36d4760c6
gnu: perl-cworld-dekker: Drop labels from inputs. 
* gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use
G-expression and avoid references to labeled inputs.
[inputs]: Drop labels.
 2023-09-14 11:17:48 +02:00
Ricardo Wurmus
9049506d8b
gnu: python-hicmatrix: Remove custom 'check phase. 
* gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Remove custom
'check phase.
 2023-09-13 22:19:23 +02:00
Mădălin Ionel Patrașcu
2c1d86e2e0
gnu: python-hicmatrix: Remove syntax error in setup.py. 
* gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Add phase
remove-invalid-syntax.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-09-13 22:17:21 +02:00
Ricardo Wurmus
9996896dc2
gnu: Add python-peaks2utr. 
* gnu/packages/bioinformatics.scm (python-peaks2utr): New variable.
 2023-09-12 12:28:32 +02:00
Ricardo Wurmus
30ec6f2fb5
gnu: macs: Update to 2.2.9.1. 
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.9.1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase.
[native-inputs]: Move python-cython from here...
[inputs]: ...and python-numpy from here...
[propagated-inputs]: ...to here.
 2023-09-12 12:28:32 +02:00
Hilton Chain
8294f45dfc
gnu: python-cgatcore: Update to 0.6.15. 
* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.15.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-09-12 08:31:23 +01:00
Navid Afkhami
2a40cd7106
gnu: r-chromunity: Update to 0.0.2-1.712e56c. 
* gnu/packages/bioinformatics.scm (r-chromunity): Update to 0.0.2-1.712e56c.
[propagated-inputs]: Add r-bsgenome-hsapiens-ucsc-hg38; remove r-skitools.
 2023-09-02 11:01:08 +02:00
Navid Afkhami
dd14ee0676
gnu: Add python-scdamandtools. 
* gnu/packages/bioinformatics.scm (python-scdamandtools): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-08-28 09:50:08 +02:00
Greg Hogan
37cca1d87e
gnu: vbz-compression: Update to 1.0.3. 
* gnu/packages/bioinformatics.scm (vbz-compression): Update to 1.0.3.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2023-08-27 19:16:45 +01:00
Ricardo Wurmus
a38ebae09c
gnu: plink: Build with GCC 8. 
* gnu/packages/bioinformatics.scm (plink)[native-inputs]: Add gcc-8.
 2023-08-10 10:26:31 +02:00
Ricardo Wurmus
17fadbb5ea
gnu: r-liana: Update to 0.1.11-1.10d8177. 
* gnu/packages/bioinformatics.scm (r-liana): Update to 0.1.11-1.10d8177.
 2023-08-04 16:18:12 +02:00
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