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* gnu: scregseg: Remove cythonized file.Efraim Flashner2022-04-14
| | | | | * gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to remove cythonized file.
* gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics).Ricardo Wurmus2022-04-14
| | | | | * gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here... * gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here.
* gnu: Add r-copykat.zimoun2022-04-11
| | | | * gnu/packages/bioinformatics.scm (r-copykat): New variable.
* gnu: smithwaterman: Fix cross-compiling.Efraim Flashner2022-04-10
| | | | | | | The 'ar' matched the 'ar' in 'aarch64-linux-gnu' to unfun consequences. * gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: More closely match the 'ar' and 'ld' commands when substituting them.
* gnu: Add r-rnaseqdtu.Hong Li2022-04-06
| | | | | | * gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: pigx-scrnaseq: Set NUMBA_CACHE_DIR.Ricardo Wurmus2022-04-05
| | | | | | | | This is needed since the update of python-loompy. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Rename 'set-PYTHONPATH to 'set-additional-environment-variables and set NUMBA_CACHE_DIR.
* gnu: pigx-scrnaseq: Use new inputs style.Ricardo Wurmus2022-04-05
| | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.
* gnu: pigx-scrnaseq: Update to 1.1.8.Ricardo Wurmus2022-04-05
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.8. [patches]: Remove. [native-inputs]: Remove. * gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: freebayes: Fix test suite.Efraim Flashner2022-04-04
| | | | * gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python.
* gnu: smithwaterman: Use new style for phases.Efraim Flashner2022-04-04
| | | | | * gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list of G-Expressions.
* gnu: smithwaterman: Fix cross-compiling.Efraim Flashner2022-04-04
| | | | | | | * gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add make-flag to use cxx-for-target. Adjust custom 'patch-source and 'build-dynamic phases to use cross toolchain binaries when cross compiling. Remove trailing #t from phases.
* gnu: python-velocyto: Set cache directory for Numba.Ricardo Wurmus2022-03-31
| | | | | * gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase 'set-numba-cache-dir.
* gnu: wfmash: Enable test suite.Efraim Flashner2022-03-31
| | | | | | * gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable tests. Add custom 'check phase based on upstream's own CI tests. [native-inputs]: Add samtools.
* gnu: Add wfmash.Arun Isaac2022-03-31
| | | | | | * gnu/packages/bioinformatics.scm (wfmash): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: htslib: Add bzip2 and xz to inputs.Arun Isaac2022-03-31
| | | | | | | | | | htslib links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz should be listed in inputs even though they are already present implicitly in native-inputs. Else, cross-compilation will fail. * gnu/packages/bioinformatics.scm (htslib)[inputs]: Add bzip2 and xz. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: python-loompy: Update to 3.0.7.Ricardo Wurmus2022-03-31
| | | | | | | | * gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7. [arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir; respect TESTS? argument in 'check phase. [propagated-inputs]: Add python-click, python-numba, and python-numpy-groupies.
* gnu: r-signac: Update to 1.6.0-2.458e647.Mădălin Ionel Patrașcu2022-03-29
| | | | | | | | * gnu/packages/bioinformatics.scm (r-signac): Update to 1.6.0-2.458e647. [propagated-inputs]: Remove r-annotationfilter, r-biocgenerics, r-biostrings, r-biovizbase, and r-ggbio; add r-qlcmatrix and r-tidyselect. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: plink-ng: Update to 2.00a3-20220315.Ricardo Wurmus2022-03-29
| | | | * gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315.
* gnu: Add r-cytobackbone.Mădălin Ionel Patrașcu2022-03-29
| | | | | | * gnu/packages/bioinformatics.scm (r-cytobackbone): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: pigx-sars-cov2-ww: Update to 0.0.5.Ricardo Wurmus2022-03-29
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5. [source]: Remove patch. [arguments]: Disable tests. * gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: pigx-rnaseq: Update to 0.0.20.Ricardo Wurmus2022-03-29
| | | | | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20. [source]: Remove patch. [inputs]: Add megadepth. * gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: Add r-scopeloomr.Ricardo Wurmus2022-03-09
| | | | * gnu/packages/bioinformatics.scm (r-scopeloomr): New variable.
* gnu: texlive-latex-pgf: Rename to "texlive-pgf".Ludovic Courtès2022-03-02
| | | | | | | | | | | | | Suggested by Ricardo Wurmus. * gnu/packages/tex.scm (texlive-latex-pgf): Rename to... (texlive-pgf): ... this. Change 'name' accordingly. (texlive-latex-pgf): Define as deprecated. (texlive-beamer)[propagated-inputs]: Use the new name. (texlive-todonotes)[propagated-inputs]: Likewise. (texlive-adjustbox)[propagated-inputs]: Likewise. (texlive-tcolorbox)[propagated-inputs]: Likewise. * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Likewise.
* gnu: minimap2: Update to 2.24.Efraim Flashner2022-02-27
| | | | * gnu/packages/bioinformatics.scm (minimap2): Update to 2.24.
* gnu: Add r-dyngen.Ricardo Wurmus2022-02-22
| | | | * gnu/packages/bioinformatics.scm (r-dyngen): New variable.
* gnu: python-gffutils: Update to 0.10.1.Marius Bakke2022-02-15
| | | | | | * gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.10.1. [arguments]: Remove obsolete phase. Respect TESTS? in check phase while at it.
* gnu: Add scvelo.Ricardo Wurmus2022-01-31
| | | | * gnu/packages/bioinformatics.scm (scvelo): New variable.
* gnu: python-louvain-0.6: Update to 0.7.1.Ricardo Wurmus2022-01-31
| | | | | | | | | | * gnu/packages/graph.scm (python-louvain-0.6): Update to 0.7.1. [arguments]: Add build phases 'find-igraph and 'pretend-version. [native-inputs]: Add python-setuptools-scm and python-wheel. Rename this variable... (python-louvain-0.7): ...to this, naturally. * gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Update reference to python-louvain-0.6.
* gnu: bwa-meth: Remove trailing #T from build phase.Ricardo Wurmus2022-01-31
| | | | | * gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T from build phase.
* gnu: bwa-meth: Update to 0.2.3.Ricardo Wurmus2022-01-31
| | | | * gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3.
* gnu: pigx-sars-cov2-ww: Fix Python module capture.Ricardo Wurmus2022-01-27
| | | | | | | The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[arguments]: Set PYTHONPATH variable in new build phase.
* gnu: pigx-scrnaseq: Fix Python module capture.Ricardo Wurmus2022-01-27
| | | | | | | The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Set PYTHONPATH variable in new build phase.
* gnu: pigx-bsseq: Fix Python module capture.Ricardo Wurmus2022-01-27
| | | | | | | The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Set PYTHONPATH variable in new build phase.
* gnu: pigx-chipseq: Fix Python module capture.Ricardo Wurmus2022-01-27
| | | | | | | The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Set PYTHONPATH variable in new build phase.
* gnu: pigx-rnaseq: Fix Python module capture.Ricardo Wurmus2022-01-27
| | | | | | | The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Set PYTHONPATH variable in new build phase.
* gnu: cwltool: Update to 3.1.20220119140128.Marius Bakke2022-01-22
| | | | | | * gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20220119140128. [propagated-inputs]: Change from PYTHON-RDFLIB-5 to PYTHON-RDFLIB. [native-inputs]: Remove PYTHON-RDFLIB-JSONLD.
* gnu: python-pyvcf: Build with old setuptools.Marius Bakke2022-01-22
| | | | | * gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Add PYTHON-SETUPTOOLS.
* gnu: Add r-scseqcomm.zimoun2022-01-21
| | | | * gnu/packages/bioinformatics.scm (r-scseqcomm): New variable.
* gnu: Add r-icellnet.zimoun2022-01-21
| | | | * gnu/packages/bioinformatics.scm (r-icellnet): New variable.
* gnu: samtools-0.1: Install headers and library.Ricardo Wurmus2022-01-20
| | | | | * gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add build phases 'install-library and 'install-headers.
* gnu: Add r-doubletfinder.Ricardo Wurmus2022-01-20
| | | | * gnu/packages/bioinformatics.scm (r-doubletfinder): New variable.
* gnu: python-rdflib: Update to 6.1.1.Marius Bakke2022-01-18
| | | | | | | | | | | * gnu/packages/rdf.scm (python-rdflib): Update to 6.1.1. [arguments]: Remove #:tests. Add #:phases. [native-inputs]: Change from PYTHON-NOSE to PYTHON-PYTEST. (python-rdflib-5): New variable. (python2-rdflib): Inherit from PYTHON-RDFLIB-5. * gnu/packages/python-xyz.scm (python-prov): Change from PYTHON-RDFLIB to PYTHON-RDFLIB-5. * gnu/packages/bioinformatics.scm (cwltool): Likewise.
* Merge branch 'version-1.4.0'Maxim Cournoyer2022-01-17
|\ | | | | | | | | | | | | With resolved conflicts in: gnu/packages/gnome.scm gnu/packages/openstack.scm gnu/packages/python-xyz.scm
| * gnu: clipper: Remove obsolete phase.Sarah Morgensen2022-01-10
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
| * gnu: python-biom-format: Remove obsolete phase.Sarah Morgensen2022-01-10
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-biom-format)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
| * gnu: python-pysam: Update to 0.18.0.Maxim Cournoyer2022-01-10
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0. [source]: Add FIXME to clarify bundled libraries in use. [phases]{check}: Streamline. [propagated-inputs]: Use latest htslib (1.14). [native-inputs]: Use latest samtools and bcftools (1.14). Remove python-nose.
| * gnu: bcftools: Update to 1.14.Maxim Cournoyer2022-01-10
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.14. (bcftools-1.12): New variable. (bcftools-1.10): Use package/inherit and delete trailing #t. [name]: Delete field.
| * gnu: samtools: Update to 1.14.Maxim Cournoyer2022-01-10
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.14. [modules]: Delete argument. [phases]{install-library, install-headers}: Delete phases. This version no longer includes the legacy library (it links to htslib directly). (samtools-1.12): New variable.
| * gnu: htslib: Update to 1.14.Maxim Cournoyer2022-01-10
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.14. (htslib-1.12): New variable. (htslib-1.10, htslib-1.9, htslib-1.3) (htslib-for-samtools-1.2): Normalize style.
* | gnu: sambamba: Update to 0.8.2.Ricardo Wurmus2022-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.2. [arguments]: Sett CC and D_LD in build phase. [native-inputs]: Add ld-gold-wrapper and binutils-gold.
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