Ricardo Wurmus
6754eb339c
gnu: delly: Simplify.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (samblaster): Update to 0.1.26.
2023-05-12 22:31:22 +02:00
Ricardo Wurmus
6331e41cde
gnu: samblaster: Simplify.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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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.
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* 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.
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* gnu/packages/bioinformatics.scm (homer): New variable.
2023-05-08 18:50:38 +02:00
Ricardo Wurmus
94d0efffb3
Revert "gnu: Add python-gimmemotifs."
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This reverts commit dc8b3ebe5d
2023-05-05 22:34:30 +02:00
Ricardo Wurmus
dc8b3ebe5d
gnu: Add python-gimmemotifs.
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* gnu/packages/bioinformatics.scm (python-gimmemotifs): New variable.
2023-05-05 15:39:29 +02:00
Ricardo Wurmus
931650212a
gnu: Add python-biofluff.
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* gnu/packages/bioinformatics.scm (python-biofluff): New variable.
2023-05-05 15:39:29 +02:00
Ricardo Wurmus
0b5088a2a3
gnu: Add python-genomepy.
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* gnu/packages/bioinformatics.scm (python-genomepy): New variable.
2023-05-05 15:39:29 +02:00
Ricardo Wurmus
181714e5f8
gnu: Add python-logomaker.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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"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.
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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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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
