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nafkhamdc
951a1433f3
gnu: Add r-illuminahumanmethylationepicmanifest. 
* gnu/packages/bioinformatics.scm (r-illuminahumanmethylationepicmanifest): New variable.

Change-Id: I9635033ed5e7e44ecfaff76cd002379582900686
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-13 14:46:51 +01:00
Mădălin Ionel Patrașcu
4c17016019
gnu: Add r-ewastools. 
* gnu/packages/bioinformatics.scm (r-ewastools): New variable.

Change-Id: I4117dbee188c7d9547fe63b2b89ec9258bbda60b
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-04 17:03:24 +01:00
Mădălin Ionel Patrașcu
e16d152463
gnu: Add r-dnamcrosshyb. 
* gnu/packages/bioinformatics.scm (r-dnamcrosshyb): New variable.

Change-Id: I19e332e6adf0ce9cc721d89bb74a1aa709778873
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-04 16:30:11 +01:00
Ricardo Wurmus
b30127052e
gnu: r-readwriter: Update to 0.3.2-1.12d32cb. 
* gnu/packages/bioinformatics.scm (r-readwriter): Update to 0.3.2-1.12d32cb.

Change-Id: I412190ce94bee4e7b5fce27db7ef8a72188e74f4
 2023-11-03 22:49:28 +01:00
Afkhami, Navid
c9361460de
gnu: Add r-miamiplot. 
* gnu/packages/bioinformatics.scm (r-miamiplot): New variable.

Change-Id: I41a3a951c6f1835800301e4c168eeeb0dd299f06
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-03 14:10:13 +01:00
Afkhami, Navid
b963bf6b1d
gnu: python-baltica: Add missing R inputs. 
* gnu/packages/bioinformatics.scm (python-baltica)[propagated-inputs]: Add
r-biocmanager, r-dplyr, r-genomicranges, r-here, r-openxlsx, r-optparse,
r-readr, r-rsamtools, r-stringr, r-tidyr, r-upsetr, and r-yaml.
[description]: Add an extra space after a period.

Change-Id: I8c1bb556048b406b95e081155a46da17a6be5676
 2023-10-31 22:03:24 +01:00
Ricardo Wurmus
5d79012073
gnu: Add r-voltron. 
* gnu/packages/bioinformatics.scm (r-voltron): New variable.

Change-Id: I5f70cf613bf2c26c4ca119483c9ad3b0beba6502
 2023-10-30 10:48:16 +01:00
Sharlatan Hellseher
4bb570a298
gnu: go-gopkg-in-check-v1: Move to (gnu packages golang-check). 
* gnu/packages/golang.scm (go-gopkg-in-check-v1): Move from here...
* gnu/packages/golang-check.scm (go-gopkg-in-check-v1): ... to here.

* gnu/packages/bioinformatics.scm: Add (gnu-packages golang-check) to
use-module.

Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
 2023-10-22 22:17:28 -04:00
Efraim Flashner
af89b109db
gnu: transanno: Don't set #:tests to #true. 
* gnu/packages/bioinformatics.scm (transanno)[arguments]: Don't set
tests unconditionally to #true.
 2023-10-22 20:25:39 +03:00
Efraim Flashner
003dc790fd
Revert "build: cargo-build-system: Disable tests by default." 
This reverts commit 37667443074a6de29f7665868f102111d62f0af9.

This change needs more discussion.
 2023-10-18 11:36:31 +03:00
Efraim Flashner
4fcf042532
gnu: transanno: Fix build. 
* gnu/packages/bioinformatics.scm (transanno)[arguments]: Run the test
suite.  Don't patch Cargo.toml in liftover-rs. Don't patch crate in
vendor-dir.
[native-inputs]: Add pkg-config.
[inputs]: Add xz.
 2023-10-18 11:36:31 +03:00
Efraim Flashner
d631d901d8
build: cargo-build-system: Disable tests by default. 
* guix/build-system/cargo.scm (cargo-build): Disable tests by default.
* gnu/packages/admin.scm (greetd, wlgreet, du-dust),
* gnu/packages/bioinformatics.scm (circtools, python-gseapy),
* gnu/packages/crypto.scm (rust-minisign, b3sum),
* gnu/packages/gnome.scm (librsvg),
* gnu/packages/python-crypto.scm (python-blake3,
python-cryptography-rust),
* gnu/packages/python-xyz.scm (python-orjson),
* gnu/packages/rust-apps.scm (agate, alfis, bat, diffr, drill, dutree,
exa, fd, hexyl, hyperfine, i3status-rust, just, maturin, ripgrep, rot8,
rust-swc, rust-cargo-edit, git-interactive-rebase-tool, rust-cbindgen,
rust-cbindgen-0.24, rust-cbindgen-0.19, sniffglue, tectonic, treefmt,
hex, tokei, vivid, watchexec, rbw, rust-analyzer, rust-cargo-c, rtss,
skim, skim-0.7, svd2rust, swayhide, tealdeer, git-absorb, zoxide, htmlq),
* gnu/packages/sequoia.scm (sequoia-sqv),
* gnu/packages/syndication.scm (newsboat),
* gnu/packages/terminals.scm (alacritty),
* gnu/packages/text-editors.scm (kak-lsp, parinfer-rust),
* gnu/packages/tree-sitter.scm (tree-sitter-cli),
* gnu/packages/video.scm (rav1e),
* gnu/packages/web.scm (monolith, castor)
[arguments]: Enable tests.
 2023-10-18 11:36:18 +03:00
Afkhami, Navid
48f9484483
gnu: Add r-metacell. 
* gnu/packages/bioinformatics.scm (r-metacell): New variable.
 2023-10-17 14:25:36 +02:00
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