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Author SHA1 Message Date
Ricardo Wurmus
0bf3c9abaa
gnu: metabat: Update to 2.15. 
* gnu/packages/bioinformatics.scm (metabat): Update to 2.15.
[source]: Remove patch.
[build-system]: Use cmake-build-system.
[arguments]: Adjust to new build system.
* gnu/packages/patches/metabat-fix-compilation.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-12-09 11:50:10 +01:00
Ricardo Wurmus
ab445eb4b7
gnu: python2-scikit-learn: Disable one more test. 
* gnu/packages/machine-learning.scm (python2-scikit-learn)[arguments]: Do not
inherit; remove obsolete 'make-files-writable phase; disable one more failing
test in 'check phase.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
1c7914009a
gnu: seek: Update to 1-1.196ed4c. 
* gnu/packages/bioinformatics.scm (seek): Update to 1-1.196ed4c.
[source]: Fetch from github.
[build-system]: Use cmake-build-system.
[arguments]: Remove all custom phases; replace 'check phase; disable tests;
set configure flags.
[inputs]: Add apache-thrift:include, apache-thrift:lib, and python.
[native-inputs]: Remove autoconf, automake, and perl; add pkg-config.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
4fb363c906
gnu: libsvm: Install header and library. 
* gnu/packages/machine-learning.scm (libsvm)[arguments]: Add build phase
'build-lib; also install header file and shared library in the 'install phase.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
26e26bc819
gnu: miso: Update to 0.5.4-1.b714021. 
* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4-1.b714021.
[source]: Fetch via git; simplify snippet.
[inputs]: Replace samtools with samtools-1.2.
[home-page]: Update to new location.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
0b8a75cc3a
gnu: Add samtools-1.2. 
* gnu/packages/bioinformatics.scm (samtools-1.2): New variable.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
f505f588a7
gnu: Add htslib-for-samtools-1.2. 
* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2): New variable.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
3ebcd637a5
gnu: python2-scipy: Override native inputs. 
* gnu/packages/python-science.scm (python2-scipy)[native-inputs]: Override;
replace gfortran with gfortran-7; add gcc-7.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
3cd37c94bd
gnu: python2-matplotlib: Fix mpl_toolkits module. 
* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Add phase
'create-init-file; restore 'sanity-check phase.
 2021-12-09 11:17:45 +01:00
Ricardo Wurmus
b69156ef30
gnu: Add gfortran-7. 
* gnu/packages/gcc.scm (gfortran-7): New variable.
 2021-12-09 11:17:45 +01:00
Ludovic Courtès
95a4965f2d
gnu: python-slepc4py: Update to 3.16.1. 
This is a followup 5b4d1e57b6.

* gnu/packages/maths.scm (slepc-openmpi)[inputs]: Move ARPACK-NG-OPENMPI to...
[propagated-inputs]: ... here.
(python-slepc4py): Update to 3.16.1.
 2021-12-08 23:04:00 +01:00
Ludovic Courtès
fe55ae488b
gnu: python-petsc4py: Update to 3.16.1. 
This is a followup to 07ac13a26a.

* gnu/packages/maths.scm (python-petsc4py): Update to 3.16.1.
 2021-12-08 22:59:44 +01:00
Ludovic Courtès
3b8825421b
gnu: geeqie: Fix X11 error at startup. 
Fixes <https://issues.guix.gnu.org/52089>.
Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>.
Patch provided by John Kehayias <john.kehayias@protonmail.com>.

* gnu/packages/patches/geeqie-clutter.patch: New file.
* gnu/packages/image-viewers.scm (geeqie)[sources]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2021-12-08 22:35:03 +01:00
Ludovic Courtès
77c8382bb6
gnu: mumps: Allow compilation with GCC 10. 
Following the suggestion at
<https://community.freefem.org/t/compline-on-macos-10-15-6/543>.

* gnu/packages/maths.scm (mumps)[arguments]: In 'configure' phase, add
'-fallow-argument-mismatch' to 'OPTF'.
 2021-12-08 18:56:53 +01:00
Ludovic Courtès
3867cb7885
maint: Don't require unsupported packages such as GNOME on i686-linux. 
* etc/release-manifest.scm (%system-manifest): Filter out PACKAGE when
it doesn't pass 'supported-package?'.
 2021-12-08 18:56:52 +01:00
Ludovic Courtès
49599fab56
services: %desktop-services: Use SDDM rather than GDM on non-x86_64. 
This works around the fact that Rust is currently unavailable in Guix on
platforms other than x86_64-linux:

  https://lists.gnu.org/archive/html/guix-devel/2021-11/msg00197.html

* gnu/services/desktop.scm (desktop-services-for-system): New
procedure.
(%desktop-services): Turn into a macro.
 2021-12-08 18:56:52 +01:00
Ludovic Courtès
24ead149db
system: Mark 'services' field as thunked. 
This allows us to make services dependent on (%current-system), for
example.

* gnu/system.scm (<operating-system>)[services]: Mark as thunked.
 2021-12-08 18:56:47 +01:00
Ludovic Courtès
20e6446a68
gnu: idutils: Fix build with glibc 2.33. 
* gnu/packages/idutils.scm (idutils)[source]: Remove reference to 'gets'
from "lib/stdio.in.h".
 2021-12-08 18:55:58 +01:00
Efraim Flashner
a59abcb350
gnu: libtorrent-rasterbar: Build with default cmake. 
* gnu/packages/bittorrent.scm (libtorrent-rasterbar)[arguments]: Remove
cmake flag.
 2021-12-08 17:36:35 +02:00
Ricardo Wurmus
00ae87c41a
gnu: tadbit: Update to 1.0.1-1.5c4c1dd. 
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-1.5c4c1dd.
[arguments]: Remove trailing #T from build phases; pass -fcommon to test
binaries; run tests conditionally.
 2021-12-08 16:32:37 +01:00
Ricardo Wurmus
7f4d25f86e
gnu: python2-sphinx: Remove websupport test. 
* gnu/packages/sphinx.scm (python2-sphinx)[arguments]: Remove websupport test
file.
 2021-12-08 16:13:08 +01:00
Ricardo Wurmus
68619cad28
gnu: python2-sphinxcontrib-websupport: Downgrade to 1.1.2. 
* gnu/packages/sphinx.scm (python2-sphinxcontrib-websupport): Downgrade to
1.1.2.
[arguments]: Override; delete 'sanity-check phase.
[propagated-inputs]: Override and add python2-six.
(python-sphinxcontrib-websupport)[properties]: Record python2-variant.
 2021-12-08 16:13:08 +01:00
Ricardo Wurmus
a4a7c78f68
gnu: python2-jinja2: Downgrade to 2.11.3 
* gnu/packages/python-xyz.scm (python2-jinja2): Downgrade to the last version
supporting Python 2.
(python-jinja2)[properties]: Record python2-variant.
 2021-12-08 16:13:08 +01:00
Ricardo Wurmus
14ed9b049e
gnu: python2-markupsafe: Downgrade to 1.1.1. 
* gnu/packages/python-xyz.scm (python2-markupsafe): Downgrade to 1.1.1,
because that's the last version to support Python 2.
 2021-12-08 14:43:38 +01:00
Ricardo Wurmus
c8060055de
gnu: ocaml-mcl: Add -fcommon to compiler flags. 
* gnu/packages/machine-learning.scm (ocaml-mcl)[arguments]: Add -fcommon.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
b835d10d61
gnu: paml: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (paml)[arguments]: Set CFLAGS.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
2157d82ed3
gnu: paml: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (paml)[arguments]: Remove trailing #T from
build phases.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
76b39f03d2
gnu: sambamba: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (sambamba)[arguments]: Remove trailing #T
from build phases.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
62da1b34d1
gnu: discrover: Add texlive-fonts-ec to inputs. 
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add
texlive-fonts-ec.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
62e196608c
gnu: discrover: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove trailing #T
from build phases.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
1f63c46a1c
gnu: tbsp: Update to 1.0.0-2.dc30c03. 
* gnu/packages/bioinformatics.scm (tbsp): Update to 1.0.0-2.dc30c03.
[arguments]: Relax requirement on matplot.  This may turn out to be a mistake.
[inputs]: Replace python-biopython with python-biopython-1.73.
 2021-12-08 14:31:54 +01:00
Ricardo Wurmus
1f7c06965c
gnu: mantis: Update to 0.1-2.b6979a2. 
* gnu/packages/bioinformatics.scm (mantis): Update to 0.1-2.b6979a2.
[arguments]: Disable the use of SSE4.2 instructions.
[native-inputs]: Build with GCC 7.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
738f22fa06
gnu: imp: Disable tests. 
* gnu/packages/bioinformatics.scm (imp)[arguments]: Disable unreliable test
suite.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
acfbb53222
gnu: snap-aligner: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (snap-aligner): Update to 2.0.0.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
42a7b5215b
gnu: snap-aligner: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Remove trailing #T
from 'install phase.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
7c58677a29
gnu: snap-aligner: Run tests conditionally. 
* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Respect TESTS?
option.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
298a8d0b89
gnu: khmer: Cythonize source files. 
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove generated files.
[arguments]: Add phase 'do-use-cython to patch the setup.py to generate cpp
files from Cython sources; add 'build-extensions phase; replace 'check phase.
 2021-12-08 14:31:53 +01:00
Ricardo Wurmus
9a19e8f609
gnu: cwltool: Update to 3.1.20211107152837. 
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20211107152837.
[arguments]: Adjust phase 'loosen-version-restrictions; remove trailing #T
from build phases; fix /bin/sh invocations in test files.
 2021-12-08 14:31:52 +01:00
Marius Bakke
ee03b51f6e
gnu: lollypop: Build with libsoup@2. 
* gnu/packages/gnome.scm (lollypop)[inputs]: Change from LIBSOUP to
LIBSOUP-MINIMAL-2.
 2021-12-08 08:45:11 +01:00
Marius Bakke
637735da4d
gnu: rhythmbox: Adjust inputs. 
* gnu/packages/gnome.scm (rhythmbox)[inputs]: Change from PYTHON2-PYGOBJECT to
PYTHON-PYGOBJECT. Add LIBSOUP-MINIMAL-2.
 2021-12-08 08:45:11 +01:00
Marius Bakke
14bc2ce43a
gnu: labelme: Loosen Python requirements. 
* gnu/packages/image-processing.scm (labelme)[arguments]: Patch setup.py so it
does not require a specific version of Matplotlib.
 2021-12-08 08:45:11 +01:00
Ricardo Wurmus
5fb1ba880f
gnu: newick-utils: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS.
 2021-12-07 23:27:40 +01:00
Ricardo Wurmus
ed5e6c7502
gnu: blasr: Update to 5.3.5. 
* gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5.
 2021-12-07 23:20:36 +01:00
Ricardo Wurmus
38cf62a236
gnu: blasr: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from
build phase.
 2021-12-07 23:20:36 +01:00
Ricardo Wurmus
d068de0c7d
gnu: blasr-libcpp: Update to 5.3.5. 
* gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5.
[inputs]: Add htslib.
 2021-12-07 23:20:36 +01:00
Ricardo Wurmus
b81daed2de
gnu: htseq: Update to 0.12.3. 
* gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3.
 2021-12-07 23:20:36 +01:00
Ricardo Wurmus
6eecbfb9ac
gnu: clipper: Update to 2.0.1. 
* gnu/packages/bioinformatics.scm (clipper): Update to 2.0.1.
[source]: Add snippet to remove pre-compiled files.
[arguments]: Disable tests, delete 'sanity-check phase, and add
'use-python3-for-cython phase.
 2021-12-07 23:20:36 +01:00
Ricardo Wurmus
fc797a3e8f
gnu: pbbam: Update to 1.7.0. 
* gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0.
[arguments]: Remove phase 'find-googletest; add phase 'patch-tests.
[propagated-inputs]: Add pbcopper.
 2021-12-07 23:20:30 +01:00
Ricardo Wurmus
b764d10e91
gnu: bwa-pssm: Fix build. 
* gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase
'patch-C-error.
 2021-12-07 17:53:14 +01:00
Ricardo Wurmus
4195a877cb
gnu: Add pbcopper. 
* gnu/packages/bioinformatics.scm (pbcopper): New variable.
 2021-12-07 16:00:22 +01:00