| Age | Commit message (Expand) | Author |
|---|
| 2020-03-07 | gnu: r-methylkit: Add r-knitr....* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-03-07 | gnu: r-vsn: Add r-knitr....* gnu/packages/bioinformatics.scm (r-vsn)[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-03-06 | gnu: python-scanpy: Update to 1.4.5.1....* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.5.1.
[source]: Fetch from pypi.
[propagated-inputs]: Add python-legacy-api-wrap, python-packaging,
python-patsy, and python-umap-learn.
[native-inputs]: Add python-setuptools-scm.
| Ricardo Wurmus |
| 2020-03-03 | gnu: gess: Use WRAP-SCRIPT....* gnu/packages/bioinformatics.scm (gess)[arguments]: Use WRAP-SCRIPT.
[inputs]: Add guile-3.0 for wrapper.
| Ricardo Wurmus |
| 2020-03-03 | gnu: gess: Override PYTHONPATH....* gnu/packages/bioinformatics.scm (gess)[arguments]: Override PYTHONPATH
instead of augmenting it.
| Ricardo Wurmus |
| 2020-03-02 | gnu: r-seqminer: Update to 8.0....* gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
| Ricardo Wurmus |
| 2020-03-01 | gnu: r-hdf5array: Update to 1.14.3....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
| Ricardo Wurmus |
| 2020-03-01 | gnu: r-rsamtools: Update to 2.2.3....* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
| Ricardo Wurmus |
| 2020-03-01 | gnu: r-edger: Update to 3.28.1....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
| Ricardo Wurmus |
| 2020-03-01 | gnu: r-seurat: Update to 3.1.4....* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.4.
[propagated-inputs]: Add r-patchwork.
| Ricardo Wurmus |
| 2020-02-27 | gnu: infernal: Update to 1.1.3....* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.3.
[native-inputs]: Add python.
| Ricardo Wurmus |
| 2020-02-27 | gnu: vcftools: Update to 0.1.16....* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.16.
| Ricardo Wurmus |
| 2020-02-27 | gnu: bedtools: Update to 2.29.2....* gnu/packages/bioinformatics.scm (bedtools): Update to 2.29.2.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Change to Expat.
| Ricardo Wurmus |
| 2020-02-27 | gnu: rseqc: Update to 3.0.1....* gnu/packages/bioinformatics.scm (rseqc): Update to 3.0.1.
[source]: Remove snippet.
[arguments]: Remove to build with Python 3.
[inputs]: Replace python2-cython, python2-pysam, and python2-numpy with
python-cython, python-pysam, and python-numpy, respectively; add
python-bx-python and python-pybigwig.
[native-inputs]: Replace python2-nose with python-nose.
| Ricardo Wurmus |
| 2020-02-26 | gnu: proteinortho: Update to 6.0.14....* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.0.14.
[source]: Fetch from git; remove pre-built scripts.
[arguments]: Set make-flags; update wrap-programs phase to wrap all scripts.
[inputs]: Add guile-3.0, diamond, python-wrapper, lapack, and openblas; remove
python-2.
[native-inputs]: Add which.
[license]: Update to GPLv3+
| Ricardo Wurmus |
| 2020-02-26 | gnu: diamond: Update to 0.9.30....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
| Ricardo Wurmus |
| 2020-02-26 | gnu: crossmap: Update to 0.3.8....* gnu/packages/bioinformatics.scm (crossmap): Update to 0.3.8.
[arguments]: Remove to build with default Python.
[inputs]: Add python-pybigwig; replace python2-bx-python, python2-numpy, and
python2-pysam with their Python 3 variants.
[native-inputs]: Replace python2-cython and python2-nose with their Python 3
variants.
| Ricardo Wurmus |
| 2020-02-26 | gnu: macs: Update to 2.2.6....* gnu/packages/bioinformatics.scm (macs): Update to 2.2.6.
[source]: Fetch from git.
[arguments]: Enable tests, build with default Python.
[inputs]: Replace python2-numpy with python-numpy.
[native-inputs]: Add python-pytest.
| Ricardo Wurmus |
| 2020-02-26 | gnu: Remove python-loompy-for-pigx-scrnaseq....* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove
variable.
| Ricardo Wurmus |
| 2020-02-26 | gnu: pigx-scrnaseq: Update to 1.1.3....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.3.
[arguments]: Remove.
[inputs]: Remove dropseq-tools and java-picard; add flexbar, jellyfish, and
r-seurat; replace python-loompy-for-pigx-scrnaseq with python-loompy.
| Ricardo Wurmus |
| 2020-02-25 | gnu: jamm: Update to 1.0.7.6....* gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6.
| Ricardo Wurmus |
| 2020-02-19 | gnu: r-scran: Update to 1.14.6....* gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.6.
| Ricardo Wurmus |
| 2020-02-19 | gnu: r-hdf5array: Update to 1.14.2....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.2.
| Ricardo Wurmus |
| 2020-02-19 | gnu: r-gviz: Update to 1.30.3....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.3.
| Ricardo Wurmus |
| 2020-02-19 | gnu: r-rhtslib: Update to 1.18.1....* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.1.
| Ricardo Wurmus |
| 2020-02-19 | gnu: r-genomicfeatures: Update to 1.38.2....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.2.
| Ricardo Wurmus |
| 2020-02-19 | gnu: r-rsamtools: Update to 2.2.2....* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.2.
| Ricardo Wurmus |
| 2020-02-19 | gnu: r-limma: Update to 3.42.2....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.2.
| Ricardo Wurmus |
| 2020-02-19 | gnu: r-shortread: Update to 1.44.3....* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.3.
| Ricardo Wurmus |
| 2020-02-19 | gnu: r-seurat: Update to 3.1.3....* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.3.
[propagated-inputs]: Remove r-sdmtools.
| Ricardo Wurmus |
| 2020-02-19 | gnu: r-qtl: Update to 1.45-11....* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.45-11.
| Ricardo Wurmus |
| 2020-02-18 | gn: edirect: Update to 12.1.20190829....The previous version has disappeared upstream.
* gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190829.
| Efraim Flashner |
| 2020-02-13 | gnu: python2-pbcore: Remove python2-sphinx dependency....* gnu/packages/bioinformatics.scm (python2-pbcore)[arguments]: Add #:phases.
[native-inputs]: Remove PYTHON2-SPHINX.
| Marius Bakke |
| 2020-01-27 | gnu: r-gviz: Update to 1.30.1....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.1.
| Ricardo Wurmus |
| 2020-01-27 | gnu: r-genomicfeatures: Update to 1.38.1....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.1.
| Ricardo Wurmus |
| 2020-01-27 | gnu: r-s4vectors: Update to 0.24.3....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.3.
| Ricardo Wurmus |
| 2020-01-27 | gnu: r-diversitree: Update to 0.9-13....* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-13.
| Ricardo Wurmus |
| 2020-01-27 | gnu: ocaml: Switch to ocaml 4.09 by default....Bap and earley cannot be updated as they do not support 4.09 yet. Bap requires
the janestreet packages, which cannot be upgraded as no version supports
4.09 and 4.07 at the same time. Moreover, newer versions of the
janestreet packages have a different dependency graph, which will
require a whole new set of packages. We cannot simply use
package-with-ocaml4.07 on them.
* gnu/packages/ocaml.scm (ocaml-sqlite3, ocaml-ppx-tools, ocaml-gen)
(ocaml-sedlex, ocaml-pcre, ocaml-expect, ocaml-ezjsonm, ocaml-uri)
(ocaml-piqilib, ocaml-piqi, ocaml-charinfo-width, ocaml-zed)
(ocaml-lambda-term, ocaml-utop, ocaml-ppx-inline-test, ocaml-earley)
(ocaml-merlin, ocaml-gsl, ocaml-gsl-1, ocaml-sexplib0, ocaml-parsexp)
(ocaml-sexplib, ocaml-base, ocaml-stdio, ocaml-ppxlib, ocaml-ppx-compare)
(ocaml-fieldslib, ocaml-variantslib, ocaml-ppx-fields-conv)
(ocaml-ppx-sexp-conv, ocaml-ppx-variants-conv, ocaml-ppx-custom-printf)
(ocaml-bin-prot, ocaml-ppx-hash, ocaml-ppx-enumerate, ocaml-ppx-bench)
(ocaml-ppx-here, ocaml-ppx-typerep, ocaml-ppx-sexp-value)
(ocaml-ppx-sexp-message, ocaml-ppx-pipebang, ocaml-ppx-optional)
(ocaml-ppx-optcomp, ocaml-ppx-fail, ocaml-ppx-let, ocaml-ppx-assert)
(ocaml-ppx-expect, ocaml-ppx-js-style, ocaml-ppx-typerep-conv)
(ocaml-ppx-base, ocaml-ppx-bin-prot, ocaml-ppx-jane)
(ocaml-splittable-random, ocaml-configurator, ocaml-spawn, ocaml-core)
(ocaml-core-kernel, ocaml-odoc, ocaml-fftw3, ocaml-lacaml): Rename to ...
(ocaml4.07-sqlite3, ocaml4.07-ppx-tools, ocaml4.07-gen, ocaml4.07-sedlex)
(ocaml4.07-pcre, ocaml4.07-expect, ocaml4.07-ezjsonm, ocaml4.07-uri)
(ocaml4.07-piqilib, ocaml4.07-piqi, ocaml4.07-charinfo-width)
(ocaml4.07-zed, ocaml4.07-lambda-term, ocaml4.07-utop)
(ocaml4.07-ppx-inline-test, ocaml4.07-earley, ocaml4.07-merlin)
(ocaml4.07-gsl, ocaml4.07-gsl-1, ocaml4.07-sexplib0, ocaml4.07-parsexp)
(ocaml4.07-sexplib, ocaml4.07-base, ocaml4.07-stdio, ocaml4.07-ppxlib)
(ocaml4.07-ppx-compare, ocaml4.07-fieldslib, ocaml4.07-variantslib)
(ocaml4.07-ppx-fields-conv, ocaml4.07-ppx-sexp-conv)
(ocaml4.07-ppx-variants-conv, ocaml4.07-ppx-custom-printf)
(ocaml4.07-bin-prot, ocaml4.07-ppx-hash, ocaml4.07-ppx-enumerate)
(ocaml4.07-ppx-bench, ocaml4.07-ppx-here, ocaml4.07-ppx-typerep)
(ocaml4.07-ppx-sexp-value, ocaml4.07-ppx-sexp-message)
(ocaml4.07-ppx-pipebang, ocaml4.07-ppx-optional, ocaml4.07-ppx-optcomp)
(ocaml4.07-ppx-fail, ocaml4.07-ppx-let, ocaml4.07-ppx-assert)
(ocaml4.07-ppx-expect, ocaml4.07-ppx-js-style)
(ocaml4.07-ppx-typerep-conv, ocaml4.07-ppx-base, ocaml4.07-ppx-bin-prot)
(ocaml4.07-ppx-jane, ocaml4.07-splittable-random)
(ocaml4.07-configurator, ocaml4.07-spawn, ocaml4.07-core)
(ocaml4.07-core-kernel, ocaml4.07-odoc, ocaml4.07-fftw3)
(ocaml4.07-lacaml): ... to this and use ocaml 4.07.
(bap, unison): Use ocaml-4.07.
* gnu/packages/bioinformatics.scm (pplacer): Use ocaml-4.07.
| Julien Lepiller |
| 2020-01-21 | gnu: Use HTTPS for (gnu packages bioinformatics) home pages....* gnu/packages/bioinformatics (bamm, ribodiff, python-biopython)
(discrover, hisat, hisat2, htseq, fastqc, htslib, python2-pbcore, roary)
(sortmerna, r-qtl, multiqc, r-deseq, r-fastseg, sambamba, trim-galore)
(gess, kentutils, bismark, kallisto, sailfish, python-hicexplorer)
(pplacer, python2-checkm-genome, r-velocyto)[home-page]: Use HTTPS.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: r-gage: Update home page....* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: sra-tools: Update home page....* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: raxml: Update home page....* gnu/packages/bioinformatics.scm (raxml)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: prodigal: Update home page....* gnu/packages/bioinformatics.scm (prodigal)[home-page]: Use source code repository as home page.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: miso: Update home page....* gnu/packages/bioinformatics.scm (miso)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: grit: Update home page....* gnu/packages/bioinformatics.scm (grit)[home-page]: Use source code
repository as home page.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: express-beta-diversity: Update home page....The original is not coming back:
<https://github.com/dparks1134/ExpressBetaDiversity/issues/11>.
* gnu/packages/bioinformatics.scm (express-beta-diversity)[home-page]:
Use source code repository as home page.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: dendropy: Update home page....* gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2020-01-21 | gnu: Use HTTPS for bioconductor.org....* gnu/packages/bioinformatics.scm (r-homo-sapiens)[source]: Use HTTPS.
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked,
r-cghcall, r-diffbind, r-cghbase, r-ripseeker, r-chippeakanno,
r-qdnaseq, r-marray, r-multtest)[home-page]: Likewise.
* gnu/packages/graph.scm (r-rgraphviz)[home-page]: Likewise.
| Tobias Geerinckx-Rice |
| 2020-01-19 | gnu: edirect: Use HTTPS home page....* gnu/packages/bioinformatics.scm (edirect)[home-page]: Use HTTPS.
| Tobias Geerinckx-Rice |
| 2020-01-16 | gnu: kentutils: Build with OpenSSL 1.0....* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL to
OPENSSL-1.0.
| Marius Bakke |
