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3285 Commits

Author SHA1 Message Date
Maxim Cournoyer
c30ab2c0b4
gnu: Remove pyicoteo. 
* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
 2022-05-31 14:52:19 -04:00
Maxim Cournoyer
ba09192168
gnu: Remove python2-pbcore. 
* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
 2022-05-31 14:52:19 -04:00
Maxim Cournoyer
8287979669
gnu: Remove python2-pyfaidx. 
* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
850bd0c329
gnu: Remove python2-screed. 
* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
a94bc7798a
gnu: Remove miso. 
* gnu/packages/bioinformatics.scm (miso): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
23e133a907
gnu: Remove python2-warpedlmm. 
* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
bb35b50adc
gnu: Remove poretools. 
* gnu/packages/bioinformatics.scm (poretools): Delete variable.
 2022-05-31 14:52:18 -04:00
Maxim Cournoyer
bcdd45be6f
gnu: Remove python2-dendropy. 
* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer
d2c971e67b
gnu: Remove bamm. 
* gnu/packages/bioinformatics.scm (bamm): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer
1010c05800
gnu: Remove python2-pybedtools. 
* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer
725b562962
gnu: Remove python2-htseq. 
* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer
8bcb07d089
gnu: Remove pepr. 
* gnu/packages/bioinformatics.scm (pepr): Delete variable.
 2022-05-31 14:52:17 -04:00
Maxim Cournoyer
3d63c5f1ba
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.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer
d29d50a556
gnu: Remove python2-pybigwig. 
* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer
98c4f97d18
gnu: Remove ribodiff. 
* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer
9f4c958d62
gnu: Remove grit. 
* gnu/packages/bioinformatics.scm (grit): Delete variable.
 2022-05-31 14:52:16 -04:00
Maxim Cournoyer
7963e12568
gnu: Remove python2-fastalite. 
* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable.
 2022-05-31 14:52:16 -04:00
Ricardo Wurmus
0bcd28e58c
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.
 2022-05-30 23:09:46 +02:00
Ricardo Wurmus
cb115ba722
gnu: pigx-sars-cov-2: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add
'autoreconf phase to patch build system.
 2022-05-29 00:39:19 +02:00
Ricardo Wurmus
df3e5cfa05
gnu: pigx-bsseq: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system
in 'autoreconf phase.
 2022-05-29 00:34:29 +02:00
Ricardo Wurmus
b64f4a1245
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.
 2022-05-29 00:29:19 +02:00
Ricardo Wurmus
add551f651
gnu: pigx-chipseq: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build
system.
 2022-05-29 00:18:48 +02:00
Tobias Geerinckx-Rice
b015a15c57
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.
 2022-05-22 02:00:00 +02:00
Josselin Poiret
dab819d5c4
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>
 2022-05-25 09:27:25 +02:00
Mathieu Othacehe
b55310603f
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.
 2022-05-22 15:15:33 +02:00
Arun Isaac
a1a55e5b60
gnu: fastahack: Wrap long line. 
* gnu/packages/bioinformatics.scm (fastahack): Wrap long line.
 2022-05-12 12:59:18 +05:30
Arun Isaac
aaa981f7c5
gnu: cwltool: Do not propagate inputs. 
* gnu/packages/bioinformatics.scm (cwltool)[propagated-inputs]: Move to ...
[inputs]: ... here.
 2022-05-11 10:52:45 +05:30
Arun Isaac
8d25887d87
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>
 2022-05-09 11:19:43 +03:00
Arun Isaac
9047a31152
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>
 2022-05-09 11:19:39 +03:00
Arun Isaac
9a68c07507
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>
 2022-05-09 11:19:03 +03:00
Arun Isaac
9258576eea
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>
 2022-05-09 11:18:09 +03:00
Arun Isaac
713dadf47e
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>
 2022-05-09 11:17:51 +03:00
Arun Isaac
086c7c143c
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>
 2022-05-09 11:17:25 +03:00
Arun Isaac
cbda00c499
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>
 2022-05-09 11:15:12 +03:00
Arun Isaac
a990547952
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>
 2022-05-09 11:14:18 +03:00
Arun Isaac
ff1fd3b012
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>
 2022-05-09 11:13:40 +03:00
Ricardo Wurmus
6f5cbac67d
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.
 2022-05-06 15:34:31 +02:00
Ricardo Wurmus
f550c0ccb0
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.
 2022-05-06 15:34:31 +02:00
Ricardo Wurmus
39d6c13fda
gnu: python-hic2cool: Fix build. 
* gnu/packages/bioinformatics.scm (python-hic2cool)[arguments]: Fix
incompatibility with h5py 3; disable two tests.
 2022-05-02 17:33:31 +02:00
Ricardo Wurmus
b1dd32d8e3
gnu: htslib-for-stringtie: Inherit from htslib-1.12. 
* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Inherit from
htslib-1.12.
 2022-05-02 14:35:26 +02:00
Ricardo Wurmus
5caad9f252
gnu: python-cooler: Use more recent cytoolz. 
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz-for-cooler with python-cytoolz.
 2022-05-02 13:33:16 +02:00
Ricardo Wurmus
33fe027f91
gnu: Add r-giotto. 
* gnu/packages/bioinformatics.scm (r-giotto): New variable.
 2022-04-26 09:48:14 +02:00
Efraim Flashner
ffb616b69d
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.
 2022-04-19 21:56:50 +03:00
Efraim Flashner
7034746e15
gnu: scregseg: Remove cythonized file. 
* gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to
remove cythonized file.
 2022-04-14 22:55:33 +03:00
Ricardo Wurmus
c8a6e4abbc
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.
 2022-04-14 13:35:22 +02:00
zimoun
6413d0898b
gnu: Add r-copykat. 
* gnu/packages/bioinformatics.scm (r-copykat): New variable.
 2022-04-11 16:11:45 +02:00
Efraim Flashner
96a132809f
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.
 2022-04-10 20:49:33 +03:00
Hong Li
e3e3381fdb
gnu: Add r-rnaseqdtu. 
* gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2022-04-06 11:43:46 +02:00
Ricardo Wurmus
df2dc0c416
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.
 2022-04-05 18:40:48 +02:00
Ricardo Wurmus
e721122069
gnu: pigx-scrnaseq: Use new inputs style. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.
 2022-04-05 18:40:48 +02:00