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3578 Commits

Author SHA1 Message Date
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