* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
create pkg-config file.

* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
build a shared library instead of a static one.

* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Use custom
'check phase  on aarch64-linux and armhf-linux to extend the test timeout.

* gnu/packages/xorg.scm (xpra)[inputs]: Add libx264, x265, libvpx.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

* gnu/packages/xorg.scm (xpra): Update to 4.0.6.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

* gnu/packages/mp3.scm (libid3tag)[arguments]: Add a comment about Audacity
requiring a pkg-config file for libid3tag.

* gnu/packages/mp3.scm (libmad)[arguments]: Add a comment about Audacity
requiring a pkg-config file for libmad.

* gnu/packages/guile-xyz.scm (guile-libyaml): New variable.

* gnu/packages/bioinformatics.scm (r-snapatac): New variable.

* gnu/packages/bioinformatics.scm (mafft): Update to 7.475.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

* gnu/packages/musl.scm (musl): Update to 1.2.2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

This package is widely known in select circles specifically as 'bio-vcf'.

* gnu/packages/bioinformatics.scm (ruby-bio-vcf): Rename to bio-vcf.

* gnu/packages/bioinformatics.scm (ruby-bio-vcf): New variable.

* gnu/packages/linux.scm (linux-libre-4.4-version): Update to 4.4.252.
(linux-libre-4.4-pristine-source): Update hash.

* gnu/packages/linux.scm (linux-libre-4.9-version): Update to 4.9.252.
(linux-libre-4.9-pristine-source): Update hash.

* gnu/packages/linux.scm (linux-libre-4.14-version): Update to 4.14.216.
(linux-libre-4.14-pristine-source): Update hash.

* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.168.
(linux-libre-4.19-pristine-source): Update hash.

* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.90.
(linux-libre-5.4-pristine-source): Update hash.

* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.8.
(linux-libre-5.10-pristine-source): Update hash.

* gnu/packages/search.scm (xapian, python-xapian-bindings): Update to 1.4.18.

* gnu/packages/linux.scm (iptables): Update to 1.8.7.

* gnu/packages/linux.scm (nftables): Update to 0.9.8.

* gnu/packages/linux.scm (libnftnl): Update to 1.1.9.

* gnu/packages/education.scm (ktouch): Update to 20.12.1.

* gnu/packages/maths.scm (wxmaxima): Update to 20.12.2.
[arguments]: Remove #:test-target and disable tests.  Remove 'pre-check
phase.
[native-inputs]: Remove xorg-server-for-tests.
[inputs]: Add libomp.

* gnu/packages/maths.scm (gnuplot): Update to 5.4.1.
[arguments]: Set GNUTERM in #:make-flags.

* gnu/packages/emacs-xyz.scm (emacs-org-mime): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

* gnu/packages/networking.scm (nbd): Update to 3.21.

* gnu/packages/mail.scm (mblaze): Update to 1.1.

* gnu/packages/password-utils.scm (keepassxc): Update to 2.6.3.

* gnu/packages/admin.scm (facter): Update to 4.0.49.

* gnu/packages/admin.scm (inxi-minimal): Update to 3.2.02-2.

* gnu/packages/shells.scm (oil): Update to 0.8.6.

* gnu/packages/music.scm (pd): Update to 0.51-4.

* gnu/packages/gnome.scm (libhandy): Update to 1.0.3.

* gnu/services/web.scm (php-fpm-accounts): Ensure `php-fpm` group is not
duplicated.

Signed-off-by: Leo Prikler <leo.prikler@student.tugraz.at>

* gnu/services/cups.scm (%cups-accounts): Try to reuse lp from %base-groups.

* gnu/bootloader/grub.scm (setup-gfxterm): Remove parameter font-file.
Refer to the installed font in /boot, not in the store.
(font-file): Delete obsolete function.
(install-grub): When populating a disk-image, install the unicode font, too.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>

* gnu/packages/lisp-xyz.scm (sbcl-cffi): Update to 0.23.0.

Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>

* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.3.
[source]: Add patch. Add snippet to remove vendored library.
[build-system]: Switch to meson-build-system.
[inputs]: Remove bamtools. Add fastahack, smithwaterman, tabixpp.
[native-inputs]: Remove procps, python-2, tabixpp source, smithwaterman
source, multichoose source, fsom source, filevercmp source, fastahack
source, bash-tap source. Add bash-tap, grep, pkg-config, simde, vcflib.
[arguments]: Drop make-flags. Don't delete 'configure phase. Delete
custom 'fix-tests, 'build-tabixpp-and-vcflib, 'fix-makefiles, 'install
phases. Adjust 'unpack-submodule-sources phase to changed native-inputs.
Add new 'patch-source phase.