| Age | Commit message (Expand) | Author |
|---|
| 2022-05-31 | gnu: Remove pyicoteo....* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-pbcore....* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-pyfaidx....* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-screed....* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove miso....* gnu/packages/bioinformatics.scm (miso): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-warpedlmm....* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove poretools....* gnu/packages/bioinformatics.scm (poretools): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-dendropy....* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove bamm....* gnu/packages/bioinformatics.scm (bamm): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-pybedtools....* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-htseq....* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove pepr....* gnu/packages/bioinformatics.scm (pepr): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: tetoolkit: Update to 2.2.1b....* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b.
[python]: Delete argument.
[phases]: Delete trailing #t.
{make-writable}: Delete phase.
{adjust-requirements}: New phase.
{patch-invocations}: Use search-input-file.
{wrap-program}: Use search-input-file.
[inputs]: Remove python2-argparse. Replace python2-pysam with python-pysam.
[home-page]: Update URL.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-pybigwig....* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove ribodiff....* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove grit....* gnu/packages/bioinformatics.scm (grit): Delete variable.
| Maxim Cournoyer |
| 2022-05-31 | gnu: Remove python2-fastalite....* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable.
| Maxim Cournoyer |
| 2022-05-30 | gnu: python-scanpy: Update to 1.9.1....* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.1.
[arguments]: Add phase 'set-numba-cache-dir; disable more broken tests.
[propagated-inputs]: Add python-dask and python-session-info; replace
python-louvain-0.7 with python-louvain.
| Ricardo Wurmus |
| 2022-05-29 | gnu: pigx-sars-cov-2: Fix build....* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add
'autoreconf phase to patch build system.
| Ricardo Wurmus |
| 2022-05-29 | gnu: pigx-bsseq: Fix build....* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system
in 'autoreconf phase.
| Ricardo Wurmus |
| 2022-05-29 | gnu: pigx-scrnaseq: Fix build....* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Add autoreconf
step to work around m4 macro bug and missing VERSION file.
[native-inputs]: Add autoconf and automake.
| Ricardo Wurmus |
| 2022-05-29 | gnu: pigx-chipseq: Fix build....* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build
system.
| Ricardo Wurmus |
| 2022-05-22 | gnu: Fix all this damn packages....* gnu/packages/bioinformatics.scm (r-icellnet)[description]:
Fix ‘this packages’ typo.
* gnu/packages/cran.scm (r-add2ggplot)[description]: Likewise.
* gnu/packages/crates-io.scm (rust-const-oid-0.6, rust-pem-rfc7468-0.2)
(rust-scrypt-0.8)[description]: Likewise.
| Tobias Geerinckx-Rice |
| 2022-05-25 | Move (gnu platform) and (gnu platforms ...) to guix/....* gnu/platform.scm:
* gnu/platforms/arm.scm:
* gnu/platforms/hurd.scm:
* gnu/platforms/mips.scm:
* gnu/platforms/powerpc.scm:
* gnu/platforms/riscv.scm:
* gnu/platforms/s390.scm:
* gnu/platforms/x86.scm: Move to guix/.
* Makefile.am:
* doc/guix.texi (Porting to a New Platform):
* etc/release-manifest.scm:
* gnu/ci.scm:
* gnu/image.scm:
* gnu/local.mk:
* gnu/packages/bioinformatics.scm:
* gnu/packages/bootstrap.scm:
* gnu/packages/cross-base.scm:
* gnu/packages/instrumentation.scm:
* gnu/packages/linux.scm:
* gnu/system/image.scm:
* gnu/system/images/hurd.scm:
* gnu/system/images/novena.scm:
* gnu/system/images/pine64.scm:
* gnu/system/images/pinebook-pro.scm:
* gnu/system/images/rock64.scm:
* guix/scripts/build.scm:
* guix/scripts/system.scm:
* guix/self.scm: Update (gnu platform...) to (guix platform...).
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
| Josselin Poiret |
| 2022-05-22 | linux: Remove system->linux-architecture procedure....* gnu/packages/linux.scm (system->linux-architecture): Remove it.
(make-linux-libre-headers*, make-linux-libre*): Adapt them.
* guix/build-system/linux-module.scm (system->arch): Adapt it.
* gnu/packages/instrumentation.scm (uftrace): Ditto.
* gnu/packages/cross-base.scm (cross-kernel-headers): Ditto.
* gnu/packages/bioinformatics.scm (ncbi-vdb): Ditto.
* doc/guix.texi (Porting to a new platform): Update it.
| Mathieu Othacehe |
| 2022-05-12 | gnu: fastahack: Wrap long line....* gnu/packages/bioinformatics.scm (fastahack): Wrap long line.
| Arun Isaac |
| 2022-05-11 | gnu: cwltool: Do not propagate inputs....* gnu/packages/bioinformatics.scm (cwltool)[propagated-inputs]: Move to ...
[inputs]: ... here.
| Arun Isaac |
| 2022-05-09 | gnu: vcflib: Set absolute path to pkg-config....Setting the absolute path to pkg-config is required to support
cross-compilation.
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Set
PKG_CONFIG_EXECUTABLE in #:configure-flags.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: vcflib: Find submodule sources in native-inputs during cross-compilation....* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In the
unpack-submodule-sources phase, look for submodule sources in both inputs and
native-inputs.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: vcflib: Use G-expressions....* gnu/packages/bioinformatics.scm (vcflib)[source, arguments]: Rewrite using
G-expressions.
[arguments]: Do not return #t from custom phases.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: fastahack: Use compiler specific to the build target....* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Set CXX in
#:make-flags. In the build-dynamic phase, use cxx-for-target instead of g++.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: fastahack: Use G-expressions....* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Rewrite
using G-expressions. Do not return #t from custom phases.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: tabixpp: Fix cross-compilation....tabixpp 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 (tabixpp)[inputs]: Add bzip2 and xz.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: tabixpp: Use build tools specific to the target....* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Set CC and CXX in
#:make-flags. In the build-libraries phase, use cxx-for-target instead of g++
and ar-for-target instead of ar.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: tabixpp: Use #:make-flags....* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Do not override the
build phase. Move the required make arguments to #:make-flags. Add
build-libraries phase.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-09 | gnu: tabixpp: Use G-expressions....* gnu/packages/bioinformatics.scm (tabixpp)[source]: Reindent.
[arguments]: Use search-input-file and search-input-directory.
[source, arguments]: Rewrite using G-expressions. Do not return #t from
snippets and custom phases.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-05-06 | gnu: pigx-sars-cov-2: Update to 0.0.7....* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.7.
[inputs]: Remove bbmap and prinseq; add r-viridis.
[arguments]: Remove autoreconf phase.
| Ricardo Wurmus |
| 2022-05-06 | gnu: Add pigx-sars-cov-2....* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): New variable.
(pigx-sars-cov2-ww): Deprecate this package in favor of the former.
| Ricardo Wurmus |
| 2022-05-02 | gnu: python-hic2cool: Fix build....* gnu/packages/bioinformatics.scm (python-hic2cool)[arguments]: Fix
incompatibility with h5py 3; disable two tests.
| Ricardo Wurmus |
| 2022-05-02 | gnu: htslib-for-stringtie: Inherit from htslib-1.12....* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Inherit from
htslib-1.12.
| Ricardo Wurmus |
| 2022-05-02 | gnu: python-cooler: Use more recent cytoolz....* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz-for-cooler with python-cytoolz.
| Ricardo Wurmus |
| 2022-04-26 | gnu: Add r-giotto....* gnu/packages/bioinformatics.scm (r-giotto): New variable.
| Ricardo Wurmus |
| 2022-04-19 | gnu: vcflib: Update to 1.0.3....* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.3.
[source]: Remove trailing #t.
[arguments]: Remove trailing #t from phases.
| Efraim Flashner |
| 2022-04-14 | gnu: scregseg: Remove cythonized file....* gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to
remove cythonized file.
| Efraim Flashner |
| 2022-04-14 | gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics)....* gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here...
* gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here.
| Ricardo Wurmus |
| 2022-04-11 | gnu: Add r-copykat....* gnu/packages/bioinformatics.scm (r-copykat): New variable.
| zimoun |
| 2022-04-10 | gnu: smithwaterman: Fix cross-compiling....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.
| Efraim Flashner |
| 2022-04-06 | gnu: Add r-rnaseqdtu....* gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Hong Li |
| 2022-04-05 | gnu: pigx-scrnaseq: Set NUMBA_CACHE_DIR....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.
| Ricardo Wurmus |
| 2022-04-05 | gnu: pigx-scrnaseq: Use new inputs style....* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.
| Ricardo Wurmus |
