| Age | Commit message (Expand) | Author |
|---|
| 2023-09-26 | multiqc: Don't propagate inputs....* gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Move all
packages ...
[inputs]: ... to here.
| Efraim Flashner |
| 2023-09-24 | gnu: python-pygenometracks: Remove syntax error in setup.py....* gnu/packages/bioinformatics.scm (python-pygenometracks)[arguments]:
Add phase remove-invalid-syntax.
| Mădălin Ionel Patrașcu |
| 2023-09-24 | gnu: htslib: Link against htscodecs....* gnu/packages/bioinformatics.scm (htslib)[source]: Add snippet to
remove bundled htscodecs.
[arguments]: Add configure-flag to link against htscodecs.
[propagated-inputs]: Add htscodecs.
(htslib-1.14, htslib-1.12): Use bundled htscodecs.
| Efraim Flashner |
| 2023-09-24 | gnu: htscodecs: Update to 1.5.1....* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.5.1.
| Efraim Flashner |
| 2023-09-22 | gnu: wfa2-lib: Mark package as tunable....* gnu/packages/bioinformatics.scm (wfa2-lib)[properties]: New field.
| Efraim Flashner |
| 2023-09-22 | gnu: python-bwapy: Fix typo....* gnu/packages/bioinformatics.scm (python-bwapy)[synopsis]: Fix typo.
| Marius Bakke |
| 2023-09-22 | gnu: python-arboreto: Add missing inputs....* gnu/packages/bioinformatics.scm (python-arboreto)[propagated-inputs]: Add
PYTHON-LZ4 and PYTHON-PYARROW.
| Marius Bakke |
| 2023-09-20 | gnu: wfmash: Update to 0.10.5....* gnu/packages/bioinformatics.scm (wfmash): Update to 0.10.5.
[source]: Update to changes in source code.
[arguments]: Add configure-flag to enable more features.
[native-inputs]: Add pkg-config.
| Efraim Flashner |
| 2023-09-18 | gnu: python-plastid: Patch it for python 3.10....* gnu/packages/bioinformatics.scm (python-plastid)[arguments]: Add new phase
'patch-for-python-3.10.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2023-09-14 | gnu: perl-cworld-dekker: Drop labels from inputs....* gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use
G-expression and avoid references to labeled inputs.
[inputs]: Drop labels.
| Ricardo Wurmus |
| 2023-09-13 | gnu: python-hicmatrix: Remove custom 'check phase....* gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Remove custom
'check phase.
| Ricardo Wurmus |
| 2023-09-13 | gnu: python-hicmatrix: Remove syntax error in setup.py....* gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Add phase
remove-invalid-syntax.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2023-09-12 | gnu: Add python-peaks2utr....* gnu/packages/bioinformatics.scm (python-peaks2utr): New variable.
| Ricardo Wurmus |
| 2023-09-12 | gnu: macs: Update to 2.2.9.1....* gnu/packages/bioinformatics.scm (macs): Update to 2.2.9.1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase.
[native-inputs]: Move python-cython from here...
[inputs]: ...and python-numpy from here...
[propagated-inputs]: ...to here.
| Ricardo Wurmus |
| 2023-09-12 | gnu: python-cgatcore: Update to 0.6.15....* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.15.
Signed-off-by: Christopher Baines <mail@cbaines.net>
| Hilton Chain |
| 2023-09-02 | gnu: r-chromunity: Update to 0.0.2-1.712e56c....* gnu/packages/bioinformatics.scm (r-chromunity): Update to 0.0.2-1.712e56c.
[propagated-inputs]: Add r-bsgenome-hsapiens-ucsc-hg38; remove r-skitools.
| Navid Afkhami |
| 2023-08-28 | gnu: Add python-scdamandtools....* gnu/packages/bioinformatics.scm (python-scdamandtools): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-08-27 | gnu: vbz-compression: Update to 1.0.3....* gnu/packages/bioinformatics.scm (vbz-compression): Update to 1.0.3.
Signed-off-by: Christopher Baines <mail@cbaines.net>
| Greg Hogan |
| 2023-08-10 | gnu: plink: Build with GCC 8....* gnu/packages/bioinformatics.scm (plink)[native-inputs]: Add gcc-8.
| Ricardo Wurmus |
| 2023-08-04 | gnu: r-liana: Update to 0.1.11-1.10d8177....* gnu/packages/bioinformatics.scm (r-liana): Update to 0.1.11-1.10d8177.
| Ricardo Wurmus |
| 2023-07-30 | gnu: mash: Fix build....* gnu/packages/bioinformatics.scm (mash)[arguments]: Add a
new 'bootstrap phase.
| Tobias Geerinckx-Rice |
| 2023-07-30 | gnu: mash: Update package style....* gnu/packages/bioinformatics.scm (mash)[arguments]: Consolidate
similar SUBSTITUTE* calls. Don't explicitly return #t from phases.
| Tobias Geerinckx-Rice |
| 2023-08-01 | gnu: Add python-baltica....* gnu/packages/bioinformatics.scm (python-baltica): New variable.
| Navid Afkhami |
| 2023-07-31 | gnu: Add python-liana-py....* gnu/packages/bioinformatics.scm (python-liana-py): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 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 |
