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Author SHA1 Message Date
Ricardo Wurmus
d84bedd830
gnu: Add python-cellbender. 
* gnu/packages/bioinformatics.scm (python-cellbender): New variable.
 2022-07-09 10:37:22 +02:00
Ricardo Wurmus
6211ecfec8
gnu: Add hh-suite. 
* gnu/packages/bioinformatics.scm (hh-suite): New variable.
 2022-07-06 14:00:21 +02:00
Ricardo Wurmus
a0125732ef
gnu: Add r-sccustomize. 
* gnu/packages/bioinformatics.scm (r-sccustomize): New variable.
 2022-07-04 13:48:58 +02:00
Thiago Jung Bauermann
4d77072c56
gnu: libsbml: Use regular check. 
* gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Replace check-0.14
with check.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2022-07-02 11:28:28 +02:00
Ricardo Wurmus
81cf674a5d
gnu: Add python-ikarus. 
* gnu/packages/bioinformatics.scm (python-ikarus): New variable.
 2022-07-01 14:54:26 +02:00
Ricardo Wurmus
f700223c3b
gnu: Add pyscenic. 
* gnu/packages/bioinformatics.scm (pyscenic): New variable.
 2022-06-16 15:20:59 +02:00
Ricardo Wurmus
3535d8dc5a
gnu: Add python-arboreto. 
* gnu/packages/bioinformatics.scm (python-arboreto): New variable.
 2022-06-16 15:20:59 +02:00
Ricardo Wurmus
fbe5707b73
gnu: Add python-ctxcore. 
* gnu/packages/bioinformatics.scm (python-ctxcore): New variable.
 2022-06-16 15:20:59 +02:00
Vagrant Cascadian
b483ef1a88
gnu: python-pybedtools: Update to 0.9.0. 
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.9.0.
  [description]: Update to satisfy guix lint.
  [license]: Update to expat and lgpl2.1+.
 2022-06-09 23:10:15 -07:00
Vagrant Cascadian
964cdd57fa
gnu: discrover: Use reproducible timestamps. 
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add
  'set-force-source-date phase.
 2022-06-06 15:08:18 -07:00
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