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3250 Commits

Author SHA1 Message Date
Ricardo Wurmus
b540e5e6bb
gnu: pigx-scrnaseq: Update to 1.1.9. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.9.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
 2022-06-01 12:57:22 +02:00
Ricardo Wurmus
93c97bfffb
gnu: pigx-bsseq: Update to 0.1.7. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.7.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove automake and autoconf.
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2022-06-01 12:41:59 +02:00
Ricardo Wurmus
6e54ce9ca9
gnu: pigx-chipseq: Update to 0.1.0. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.1.0.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
 2022-06-01 12:19:48 +02:00
Ricardo Wurmus
cd95d7ddd1
gnu: pigx-rnaseq: Update to 0.1.0. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0.
[arguments]: Remove phase 'patch-knitr.
 2022-06-01 11:07:27 +02:00
Ricardo Wurmus
0aae2f7f01
gnu: pigx-rnaseq: Update to 0.0.21. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.21.
 2022-06-01 10:46:00 +02:00
Ricardo Wurmus
0c26c8da9d
gnu: pigx-rnaseq: Fix build. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr.
 2022-06-01 10:46:00 +02:00
Ricardo Wurmus
b279e778ab
gnu: Add sylamer. 
* gnu/packages/bioinformatics.scm (sylamer): New variable.
 2022-06-01 00:17:05 +02:00
Maxim Cournoyer
c35e508b4a
gnu: Remove python2-biopython. 
* gnu/packages/bioinformatics.scm (python2-biopython): Delete variable.
 2022-05-31 14:54:17 -04:00
Maxim Cournoyer
ad030a0b7d
gnu: Remove pplacer-scripts. 
* gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable.
 2022-05-31 14:54:17 -04:00
Maxim Cournoyer
d397cb6207
gnu: Remove pplacer. 
* gnu/packages/bioinformatics.scm (pplacer): Delete variable.
 2022-05-31 14:54:16 -04:00
Maxim Cournoyer
026fca8b5b
gnu: Remove python2-checkm-genome. 
* gnu/packages/bioinformatics.scm (python2-checkm-genome): Delete variable.
 2022-05-31 14:54:15 -04:00
Maxim Cournoyer
4d7bb37981
gnu: Remove fraggenescan. 
* gnu/packages/bioinformatics.scm (fraggenescan): Delete variable.
 2022-05-31 14:54:02 -04:00
Maxim Cournoyer
6792b0b6cd
gnu: Remove python2-pysam. 
* gnu/packages/bioinformatics.scm (python2-pysam): Delete variable.
 2022-05-31 14:53:35 -04:00
Maxim Cournoyer
955e7d628d
gnu: Remove find-circ. 
* gnu/packages/bioinformatics.scm (find-circ): Delete variable.
 2022-05-31 14:53:34 -04:00
Maxim Cournoyer
a5e29cd838
gnu: Remove gess. 
* gnu/packages/bioinformatics.scm (gess): Delete variable.
 2022-05-31 14:53:34 -04:00
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