| Age | Commit message (Expand) | Author |
|---|
| 2023-07-31 | gnu: python-decoupler-py: Update to 1.5.0-1.459b235....* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to
1.5.0-1.459b235.
[arguments]: Disable two more tests.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-07-23 | gnu: fuse@3: Bind to default FUSE variable....* gnu/packages/linux.scm (fuse): Rename this…
(fuse-2): …to this, and…
(fuse-3): …rename this…
(fuse): …to this!
(fuse-static): Rename this…
(fuse-2-static): …to this.
Adjust all users.
| Tobias Geerinckx-Rice |
| 2023-07-21 | gnu: newick-utils: Skip tests when cross-compiling....* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Adjust
#: tests? to skip tests when cross-compiling.
| Efraim Flashner |
| 2023-07-18 | gnu: discrover: Fix build....* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add
TEXLIVE-FORLOOP, TEXLIVE-LISTOFITEMS, TEXLIVE-READARRAY.
| Nicolas Goaziou |
| 2023-07-18 | gnu: Rationalize texlive-updmap.cfg and texlive-tiny inputs....TEXLIVE-UPDMAP.CFG and TEXLIVE-TINY should only be used as native inputs.
Also remove texlive packages already provided by them.
* doc/build.scm (pdf-manual):
* gnu/packages/algebra.scm (pari-gp):
* gnu/packages/bioinformatics.scm (discrover):
(phyml):
(velvet):
* gnu/packages/chemistry.scm (yaehmop):
* gnu/packages/chez.scm (stex-bootstrap):
(chez-web):
(chez-sockets):
* gnu/packages/cran.scm (r-prereg):
* gnu/packages/docbook.scm (dblatex):
* gnu/packages/emacs-xyz.scm (emacs-auctex):
* gnu/packages/engineering.scm (fastcap):
* gnu/packages/fsf.scm (book-faif):
* gnu/packages/graphviz.scm (dot2tex):
* gnu/packages/maths.scm (hypre):
* gnu/packages/ocaml.scm (unison):
(ocaml-bibtex2html):
* gnu/packages/plotutils.scm (asymptote):
* gnu/packages/python-xyz.scm (python-nbconvert):
(python-pypandoc):
* gnu/packages/radio.scm (gnuradio):
(libosmo-dsp):
* gnu/packages/statistics.scm (r-with-tests):
* gnu/packages/tex.scm (texlive-makecmds):
(texlive-innerscript):
(teximpatient):
(texlive-xkeyval): Remove texlive packages already provided by
TEXLIVE-UPDMAP.CFG. Don't add TEXLIVE-TINY or TEXLIVE-UPDMAP.CFG as inputs.
| Nicolas Goaziou |
| 2023-07-18 | gnu: phyml: Fix build....* gnu/packages/bioinformatics.scm (phyml)[native-inputs]: Add
TEXLIVE-INFWARERR, TEXLIVE-KVOPTIONS and TEXLIVE-PDFTEXCMDS.
| Nicolas Goaziou |
| 2023-07-18 | gnu: velvet: Improve package style....* gnu/packages/bioinformatics.scm (velvet)[arguments]: Use G-expressions.
[native-inputs]: Remove label.
| Nicolas Goaziou |
| 2023-07-18 | gnu: velvet: Fix error when building documentation....* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add TEXLIVE-GRFEXT,
TEXLIVE-INFWARERR, TEXLIVE-KVOPTIONS and TEXLIVE-KPDFTEXCMDS.
| Nicolas Goaziou |
| 2023-07-18 | gnu: texlive-latex-examplep -> texlive-examplep....* gnu/packages/tex.scm (texlive-examplep): New variable.
(texlive-latex-examplep): Deprecate variable.
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use new name.
| Nicolas Goaziou |
| 2023-07-18 | gnu: texlive-latex-verbatimbox -> texlive-verbatimbox....* gnu/packages/tex.scm (texlive-verbatimbox): New variable.
(texlive-latex-verbatimbox): Deprecate variable.
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use new name.
| Nicolas Goaziou |
| 2023-07-18 | gnu: texlive-fonts-ec -> texlive-ec....* gnu/packages/tex.scm (texlive-ec): New variable.
(texlive-fonts-ec): Deprecate variable.
(lyx):
(biber):
* gnu/packages/python-xyz.scm (python-pypandoc):
* gnu/packages/statistics.scm (r-with-tests):
* doc/build.scm (pdf-manual):
* gnu/packages/bioinformatics.scm (discrover):
(phyml):
(velvet):
* gnu/packages/chemistry.scm (yaehmop):
* gnu/packages/chez.scm (stex-bootstrap):
* gnu/packages/ocaml.scm (unison):
(ocaml-bibtex2html):
* gnu/packages/plotutils.scm (asymptote): Use new name.
| Nicolas Goaziou |
| 2023-07-18 | gnu: texlive-latex-psfrag -> texlive-psfrag....* gnu/packages/tex.scm (texlive-psfrag): New variable.
(texlive-latex-psfrag): Deprecate variable.
(texlive-pstool):
* gnu/packages/bioinformatics.scm (phyml): Use new name.
| Nicolas Goaziou |
| 2023-07-18 | gnu: texlive-latex-natbib -> texlive-natbib....* gnu/packages/tex.scm (texlive-natbib): New variable.
(texlive-latex-natbib): Deprecate variable.
(texlive-apacite):
* gnu/packages/bioinformatics.scm (discrover):
* gnu/packages/maths.scm (hypre): Use new name.
| Nicolas Goaziou |
| 2023-07-18 | gnu: newick-utils: Skip tests on riscv64-linux....* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Skip tests
when building on riscv64-linux.
| 宋文武 |
| 2023-07-17 | gnu: Hide python-bcbio-gff/biopython-1.73....To avoid the ambiguous package specification.
* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73): Hide
package.
| Christopher Baines |
| 2023-07-15 | gnu: r-pando: Relax requirements....* gnu/packages/bioinformatics.scm (r-pando)[arguments]: Patch DESCRIPTION
file.
| Ricardo Wurmus |
| 2023-07-09 | gnu: bwa-pssm: Update home page....* gnu/packages/bioinformatics.scm (bwa-pssm)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2023-07-09 | gnu: blasr-libcpp, blasr: Use Web Archived home pages....* gnu/packages/bioinformatics.scm (blasr-libcpp, blasr)[home-page]:
Refer to Web Archive.
| Tobias Geerinckx-Rice |
| 2023-07-12 | gnu: Add r-numbat....* gnu/packages/bioinformatics.scm (r-numbat): New variable.
| Ricardo Wurmus |
| 2023-07-12 | gnu: Add r-bpcells....* gnu/packages/bioinformatics.scm (r-bpcells): New variable.
| Ricardo Wurmus |
| 2023-07-06 | gnu: r-pando: Fix hash....* gnu/packages/bioinformatics.scm (r-pando)[source]: Update hash.
| Ricardo Wurmus |
| 2023-07-06 | gnu: bismark: Update to 0.24.1....* gnu/packages/bioinformatics.scm (bismark): Update to 0.24.1.
[source]: Delete bundled plot.ly.
[arguments]: Use plain list; remove trailing #T from build phases; adjust
'replace-plotly.js phase to account for use of script tags; adjust 'install
phase to install documentation in markdown format; add 'configure phase for
replacing references to tools.
[inputs]: Add bowtie, hisat2, minimap2, and samtools.
| Ricardo Wurmus |
| 2023-07-03 | gnu: cutadapt: Update to 4.0....* gnu/packages/bioinformatics.scm (cutadapt): Update to 4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Disable a single test; remove 'always-cythonize build phase; add
phase 'fix-test.
[native-inputs]: Add python-pytest-mock and python-pytest-timeout.
| Ricardo Wurmus |
| 2023-07-03 | gnu: python-dnaio: Update to 0.10.0....* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.10.0.
[arguments]: Disable tests, because they don't exist.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-setuptools-scm; move python-xopen from here...
[propagated-inputs]: ...to here.
| Ricardo Wurmus |
| 2023-07-03 | gnu: Add r-dtmm....* gnu/packages/bioinformatics.scm (r-dtmm): New variable.
| Navid Afkhami |
| 2023-06-29 | gnu: Add rscape....* gnu/packages/bioinformatics.scm (rscape): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-06-29 | gnu: r-pando: Update to 1.0.5....* gnu/packages/bioinformatics.scm (r-pando): Update to 1.0.5.
[propagated-inputs]: Remove r-brms and r-xgboost; add r-grr and
r-matrixgenerics.
| Ricardo Wurmus |
| 2023-06-22 | gnu: sambamba: Fix building....* gnu/packages/bioinformatics.scm (sambamba)[native-inputs]: Remove
ld-gold-wrapper, bintutils-gold. Remove input labels.
| Efraim Flashner |
| 2023-06-20 | gnu: bioruby: Update to 2.0.4....* gnu/packages/bioinformatics.scm (bioruby): Update to 2.0.4.
[arguments]: Update style.
| Christopher Baines |
| 2023-06-09 | gnu: Add python-mudata....* gnu/packages/bioinformatics.scm (python-mudata): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-06-09 | gnu: Add python-mofax....* gnu/packages/bioinformatics.scm (python-mofax): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-06-06 | gnu: Add python-decoupler-py....* gnu/packages/bioinformatics.scm (python-decoupler-py): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
| Navid Afkhami |
| 2023-06-05 | gnu: python-bulkvis: Reference upstream issue....* gnu/packages/bioinformatics.scm (python-bulkvis)[arguments]: Add comment
with link to upstream issue for bokeh compatibility patch.
| Ricardo Wurmus |
| 2023-06-05 | gnu: Add python-bulkvis....* gnu/packages/bioinformatics.scm (python-bulkvis): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-06-05 | gnu: Add python-readpaf....* gnu/packages/bioinformatics.scm (python-readpaf): New variable.
| Navid Afkhami |
| 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 |
