| Age | Commit message (Expand) | Author |
|---|
| 2023-06-02 | gnu: Add r-singlet.•••* gnu/packages/bioinformatics.scm (r-singlet): New variable.
| Ricardo Wurmus |
| 2023-06-02 | gnu: Add python-cell2cell.•••* gnu/packages/bioinformatics.scm (python-cell2cell): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-06-02 | gnu: Add java-maxent.•••* gnu/packages/bioinformatics.scm (java-maxent): New variable.
| Ricardo Wurmus |
| 2023-06-01 | gnu: Add python-pyani.•••* gnu/packages/bioinformatics.scm (python-pyani): New variable.
| Ricardo Wurmus |
| 2023-06-01 | gnu: Add python-illumina-utils.•••* gnu/packages/bioinformatics.scm (python-illumina-utils): New variable.
| Ricardo Wurmus |
| 2023-06-01 | gnu: Add python-ete3.•••* gnu/packages/bioinformatics.scm (python-ete3): New variable.
| Ricardo Wurmus |
| 2023-05-26 | gnu: Add python-gseapy.•••* gnu/packages/bioinformatics.scm (python-gseapy): New variable.
| Ricardo Wurmus |
| 2023-05-19 | gnu: java-picard-1.113: Drop input package labels.•••* gnu/packages/bioinformatics.scm (java-picard-1.113)[inputs]: Drop labels.
| Ricardo Wurmus |
| 2023-05-19 | 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.
| Ricardo Wurmus |
| 2023-05-14 | gnu: discrover: Remove package labels.•••* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Remove package
labels.
| Ricardo Wurmus |
| 2023-05-14 | 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+.
| Ricardo Wurmus |
| 2023-05-14 | gnu: delly: Simplify.•••* gnu/packages/bioinformatics.scm (delly)[source]: Simplify snippet.
[arguments]: Do not use quasiquote; simplify 'install-templates phase.
| Ricardo Wurmus |
| 2023-05-14 | 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.
| Ricardo Wurmus |
| 2023-05-14 | 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.
| Ricardo Wurmus |
| 2023-05-14 | 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.
| Ricardo Wurmus |
| 2023-05-12 | gnu: jamm: Use G-expression.•••* gnu/packages/bioinformatics.scm (jamm)[arguments]: Use G-expression.
| Ricardo Wurmus |
| 2023-05-12 | 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.
| Ricardo Wurmus |
| 2023-05-12 | gnu: multichoose: Clean up.•••* gnu/packages/bioinformatics.scm (multichoos): Fix indentation.
[arguments]: Use G-expression.
| Ricardo Wurmus |
| 2023-05-12 | gnu: samblaster: Update to 0.1.26.•••* gnu/packages/bioinformatics.scm (samblaster): Update to 0.1.26.
| Ricardo Wurmus |
| 2023-05-12 | 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.
| Ricardo Wurmus |
| 2023-05-12 | 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.
| Ricardo Wurmus |
| 2023-05-12 | gnu: methyldackel: Simplify arguments.•••* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Use list, drop
argument list.
[native-inputs]: Drop package label.
| Ricardo Wurmus |
| 2023-05-12 | gnu: phast: Simplify by using G-expression.•••* gnu/packages/bioinformatics.scm (phast)[arguments]: Use G-expression and
drop trailing #T from build phases.
| Ricardo Wurmus |
| 2023-05-12 | gnu: ribotaper: Simplify with G-expression.•••* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Use G-expression and
drop trailing #T from build phase.
| Ricardo Wurmus |
| 2023-05-12 | 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.
| Ricardo Wurmus |
| 2023-05-12 | 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.
| Ricardo Wurmus |
| 2023-05-12 | gnu: Add python-mgatk.•••* gnu/packages/bioinformatics.scm (python-mgatk): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2023-05-08 | gnu: Add homer.•••* gnu/packages/bioinformatics.scm (homer): New variable.
| Ricardo Wurmus |
| 2023-05-05 | Revert "gnu: Add python-gimmemotifs."•••This reverts commit dc8b3ebe5d4ba2a39c12f62d836963ffee1e4b47.
python-gimmemotifs is not usable without proprietary third-party tools.
| Ricardo Wurmus |
| 2023-05-05 | gnu: Add python-gimmemotifs.•••* gnu/packages/bioinformatics.scm (python-gimmemotifs): New variable.
| Ricardo Wurmus |
| 2023-05-05 | gnu: Add python-biofluff.•••* gnu/packages/bioinformatics.scm (python-biofluff): New variable.
| Ricardo Wurmus |
| 2023-05-05 | gnu: Add python-genomepy.•••* gnu/packages/bioinformatics.scm (python-genomepy): New variable.
| Ricardo Wurmus |
| 2023-05-05 | gnu: Add python-logomaker.•••* gnu/packages/bioinformatics.scm (python-logomaker): New variable.
| Ricardo Wurmus |
| 2023-05-05 | gnu: python-pyfaidx: Update to 0.7.2.1.•••* 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.
| Ricardo Wurmus |
| 2023-05-04 | gnu: python-screed: Update to 1.1.2.•••* 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>
| Mădălin Ionel Patrașcu |
| 2023-05-04 | gnu: Add python-goatools.•••* gnu/packages/bioinformatics.scm (python-goatools): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-05-03 | gnu: pigx-sars-cov-2: Update to 0.0.9.•••* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.9.
| Ricardo Wurmus |
| 2023-05-03 | gnu: Add fanc.•••* gnu/packages/bioinformatics.scm (fanc): New variable.
| Ricardo Wurmus |
| 2023-04-29 | gnu: r-tictoc: Update to 1.2.•••* gnu/packages/bioinformatics.scm (r-tictoc): Update to 1.2.
| Ricardo Wurmus |
| 2023-04-27 | gnu: gdcm: Disable dependent tests.•••* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Disable tests that depend
on the output of a disabled test.
| Ricardo Wurmus |
| 2023-04-27 | gnu: freebayes: Update to 1.3.7.•••* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.7.
[arguments]: Do not use "grep -P" in tests; drop trailing #T.
| Ricardo Wurmus |
| 2023-04-27 | gnu: vcflib: Use libwfa2.pc.•••* 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.
| Ricardo Wurmus |
| 2023-04-27 | gnu: wfa2-lib: Install pkg-config file.•••* gnu/packages/bioinformatics.scm (wfa2-lib)[arguments]: Install libwfa2.pc.
| Ricardo Wurmus |
| 2023-04-27 | gnu: express: Adjust bamtools location.•••* gnu/packages/bioinformatics.scm (express)[arguments]: Modify location of
libbamtools.so in 'use-shared-boost-libs-and-set-bamtools-paths; drop trailing
#T.
| Ricardo Wurmus |
| 2023-04-26 | gnu: python-dendropy: Fix build.•••* 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.
| Ricardo Wurmus |
| 2023-04-25 | gnu: cwltool: Use pyproject-build-system.•••"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.
| Ricardo Wurmus |
| 2023-04-25 | gnu: python-schema-salad: Use pyproject-build-system.•••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.
| Ricardo Wurmus |
| 2023-04-25 | gnu: adapterremoval: Update to 2.3.3.•••* gnu/packages/bioinformatics.scm (adapterremoval): Update to 2.3.3.
[arguments]: Simplify.
[inputs]: Reformat.
| Ricardo Wurmus |
| 2023-04-25 | gnu: bedtools-2.18: Fix build.•••* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Fix operators in
'compatibility phase.
| Ricardo Wurmus |
| 2023-04-25 | gnu: hisat: Build with GCC 10.•••* gnu/packages/bioinformatics.scm (hisat)[native-inputs]: Add gcc-10.
| Ricardo Wurmus |
