gnu: pplacer: Fix build.

* gnu/packages/bioinformatics.scm (pplacer)[inputs]: Replace gsl with
gsl-static.
* gnu/packages/ocaml.scm (ocaml4.07-gsl-1)[inputs]: Same.

gnu: Add gsl-static.

* gnu/packages/maths.scm (gsl-static): New variable.

gnu: python-dendropy: Skip additional test.

* gnu/packages/bioinformatics.scm (python-dendropy)[arguments]: Adjust
custom 'skip-broken-tests phase to skip additional test.

gnu: imp: Build with default cmake.

* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove cmake flag.

gnu: repeat-masker: Update to 4.1.2-p1.

* gnu/packages/bioinformatics.scm (repeat-masker): Update to 4.1.2-p1.

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.

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.

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.

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.

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.

gnu: Add samtools-1.2.

* gnu/packages/bioinformatics.scm (samtools-1.2): New variable.

gnu: Add htslib-for-samtools-1.2.

* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2): New variable.

gnu: python2-scipy: Override native inputs.

* gnu/packages/python-science.scm (python2-scipy)[native-inputs]: Override;
replace gfortran with gfortran-7; add gcc-7.

gnu: python2-matplotlib: Fix mpl_toolkits module.

* gnu/packages/python-xyz.scm (python2-matplotlib)[arguments]: Add phase
'create-init-file; restore 'sanity-check phase.

gnu: Add gfortran-7.

* gnu/packages/gcc.scm (gfortran-7): New variable.

gnu: python-slepc4py: Update to 3.16.1.

This is a followup 5b4d1e57b6d4931f6ee2a50abf84222fe015d045.

* gnu/packages/maths.scm (slepc-openmpi)[inputs]: Move ARPACK-NG-OPENMPI to...
[propagated-inputs]: ... here.
(python-slepc4py): Update to 3.16.1.

gnu: python-petsc4py: Update to 3.16.1.

This is a followup to 07ac13a26a0d7c8319afb42c55fc2116ec44668f.

* gnu/packages/maths.scm (python-petsc4py): Update to 3.16.1.

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.

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'.

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?'.