| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove
variable.
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* 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.
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* gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6.
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* gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.6.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.2.
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* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.3.
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* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.1.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.2.
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* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.2.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.2.
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* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.3.
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* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.3.
[propagated-inputs]: Remove r-sdmtools.
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* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.45-11.
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The previous version has disappeared upstream.
* gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190829.
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* gnu/packages/bioinformatics.scm (python2-pbcore)[arguments]: Add #:phases.
[native-inputs]: Remove PYTHON2-SPHINX.
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* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.1.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.1.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.3.
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* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-13.
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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.
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* 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.
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* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
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* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
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* gnu/packages/bioinformatics.scm (raxml)[home-page]: Update.
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* gnu/packages/bioinformatics.scm (prodigal)[home-page]: Use source code repository as home page.
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* gnu/packages/bioinformatics.scm (miso)[home-page]: Update.
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* gnu/packages/bioinformatics.scm (grit)[home-page]: Use source code
repository as home page.
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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.
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* gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update.
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* 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.
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* gnu/packages/bioinformatics.scm (edirect)[home-page]: Use HTTPS.
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* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL to
OPENSSL-1.0.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.2.
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* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.2.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.2.
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* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.4.
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* gnu/packages/bioinformatics.scm (smithwaterman): Update to 0.0.0-2.2610e25.
[arguments]: Add make-flags to build static library. Adjust custom
'install phase to install static library.
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* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.1.
[source]: Download using url-fetch.
[native-inputs]: Sort alphabetically. Move perl, python ...
[inputs]: ... to here.
[arguments]: Add make-flags. Update custom 'build phase.
(tabixpp-freebayes): Remove variable.
(freebayes)[native-inputs]: Use tabixpp-source over tabixpp-freebayes.
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* gnu/packages/bioinformatics.scm (fastahack): Update to 1.0.0.
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* gnu/packages/bioinformatics.scm (intervaltree): New variable.
(vcflib, freebayes)[native-inputs]: Use packaged intervaltree's source.
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* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.0.
[source]: Add snippet to remove vendored library.
[arguments]: Adjust custom 'build phase to fix INCLUDES.
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* gnu/packages/bioinformatics.scm (bwa)[arguments]: Install static
library.
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This fixes the bug which prevented uglify-js from being defined properly, and
cascaded back to all Common Lisp packages.
* gnu/packages/bioinformatics.scm: Replace javascript module with lisp-xyz.
* gnu/packages/cran.scm: Use lisp-xyz module.
* gnu/packages/javascript.scm (uglify-js): Move from here...
* gnu/packages/lisp-xyz.scm: ... To here.
* gnu/packages/web.scm: Replace javascript module with lisp-xyz.
* guix/build-system/minify.scm: Find uglify-js in the lisp-xyz module.
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* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1.
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* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1.
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* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1.
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