* gnu/packages/bioinformatics.scm (filtlong): Delete variable.

* gnu/packages/bioinformatics.scm (r-pando): Delete variable.

* gnu/packages/bioinformatics.scm (python-episcanpy): Delete variable.

Relates-to: guix/guix#6610
Fixes: guix/guix#9926
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

* gnu/packages/bioinformatics.scm (python-bioframe): Update to
0.8.0. Use G-Expressions.
[arguments] <test-flags>: Skip 3 more tests, rewrite with "--deselect"
option.

* gnu/packages/llvm.scm (libomp, llvm, clang-runtime, clang, clang-toolchain):
Switch to llvm-22 version.
(ocaml-llvm): Use llvm-13.
(wllvm)[native-inputs]: Remove clang; add clang-13.
(emacs-clang-format)[arguments]: Use #:lisp-directory, Adjust configure
phase. Add #:test-command.
* gnu/packages/bioinformatics.scm (alignoth)[native-inputs]: Remove clang; add
clang-13.
(lammps)[inputs]: Remove libomp; add libomp-13.
* gnu/packages/bootloaders.scm (make-grub)[inputs]: Remove clang; add
clang-13.
* gnu/packages/c.scm (libdispatch)[native-inputs]: Remove clang and llvm; add
clang-13 and llvm-13.
* gnu/packages/check.scm (pedansee)[native-inputs]: Remove clang; add
clang-13.
(python-lit)[native-inputs]: Remove llvm; add llvm-13.
* gnu/packages/codex.scm (codex, codex-acp)[native-inputs]: Remove clang; add
clang-13.
* gnu/packages/compression.scm (cmix)[native-inputs]: Remove clang; add
clang-13.
* gnu/packages/cpp.scm (ccls)[native-inputs]: Remove clang and llvm; add
clang-13 and llvm-13.
* gnu/packages/darwin.scm (cctools)[inputs]: Remove clang-toolchain; add
clang-toolchain-13.
[native-inputs]: Remove clang-toolchain; add clang-toolchain-13.
* gnu/packages/debug.scm (c-vise)[inputs]: Remove clang and llvm; add clang-13
and llvm-13.
(fandango)[native-inputs]: Remove clang; add clang-13.
* gnu/packages/diffoscope.scm (diffoscope)[native-inputs]: Remove llvm; add
llvm-13.
* gnu/packages/electronics.scm (nvc)[inputs]: Remove llvm; add llvm-13.
(openroad)[inputs]: Remove libomp; add libomp-13.
* gnu/packages/emacs-xyz.scm (emacs-irony-mode-server)[inputs]: Remove clang;
add clang-13.
* gnu/packages/file-systems.scm (bcachefs-tools-minimal)[native-inputs]:
Remove clang; add clang-13.
* gnu/packages/freedesktop.scm (waypipe)[native-inputs]: Remove clang; add
clang-13.
* gnu/packages/fusion.scm (fusion)[native-inputs]: Remove clang; add clang-13.
* gnu/packages/games.scm (hedgewars)[native-inputs]: Remove clang; add
clang-13.
* gnu/packages/gnome.scm (gnome-builder)[inputs]: Remove clang and llvm; add
clang-13 and llvm-13.
* gnu/packages/gnustep.scm (libobjc2)[inputs]: Remove clang; add clang-13.
* gnu/packages/gnuzilla.scm (mozjs)[native-inputs]: Remove llvm; add llvm-13.
* gnu/packages/graphics.scm (openshadinglanguage)[native-inputs]: Remove clang
and llvm; add clang-13 and llvm-13.
(skia)[native-inputs]: Remove clang-toolchain; add clang-toolchain-13.
(tinygltf)[native-inputs]: Remove clang; add clang-13.
* gnu/packages/kde-sdk.scm (kdevelop)[inputs]: Remove clang; add clang-13.
* gnu/packages/language.scm (liblouis)[native-inputs]: Remove clang; add
clang-13.
* gnu/packages/lean.scm (lean4)[inputs]: Remove llvm; add llvm-13.
* gnu/packages/lisp.scm (carp, picolisp)[inputs]: Remove clang; add clang-13.
* gnu/packages/machine-learning.scm (ctranslate2)[native-inputs]: Remove
libomp; add libomp-13.
* gnu/packages/mail.scm (stalwart)[native-inputs]: Remove clang; add clang-13.
* gnu/packages/maths.scm (python-mathics-core)[inputs]: Remove llvm; add
llvm-13.
* gnu/packages/ocaml.scm (bap)[inputs]: Remove llvm; add llvm-13.
[native-inputs]: Remove clang; add clang-13.
[arguments]: Use this-package-input to get llvm version.
* gnu/packages/photo.scm (darktable)[inputs]: Remove libomp; add libomp-13.
[native-inputs]: Remove llvm; add llvm-13.
(ansel)[native-inputs]: Remove llvm; add llvm-13.
(photoflare)[inputs]: Remove libomp; add libomp-13.
* gnu/packages/physics.scm (cytnx)[inputs]: Remove libomp; add libomp-13.
* gnu/packages/qt.scm (clazy)[inputs]: Remove clang and llvm; add clang-13 and
llvm-13.
* gnu/packages/rust-apps.scm (c2rust, helvum, ouch, pwmenu)
(soundcloud-tui)[native-inputs]: Remove clang; add clang-13.
* gnu/packages/rust-sources.scm (rust-ring-0.17)[native-inputs]: Remove clang;
add clang-13.
* gnu/packages/sequoia.scm (sequoia-chameleon-gnupg)
(sequoia-sq, sequoia-sqv, sequoia-wot-tools)[native-inputs]: Remove clang; add
clang-13.
* gnu/packages/text-editors.scm (parinfer-rust, parinfer-rust-emacs)[inputs]:
Remove clang; add clang-13.
* gnu/packages/virtualization.scm (xen-guest-agent)[native-inputs]: Remove
clang; add clang-13.
* gnu/packages/wm.scm (niri)[inputs]: Remove clang; add clang-13.
* gnu/packages/xorg.scm (xf86-video-vmware)[inputs]: Remove llvm; add llvm-13.
(xwayland-satellite)[inputs]: Remove clang; add clang-13.

Change-Id: Ifb8f13908a9e7112466b2e966200670ddcc2f162

* gnu/packages/bioinformatics.scm (hisat2): Update to 2.2.2.
  [arguments]<#:phases>{make-deterministic}: Set the hostname to guix.
  [supported-systems]: Limit to x86_64-linux.

Merges: https://codeberg.org/guix/guix/pulls/6945
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>

* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.25.
[source]: Switch to git-fetch.

* gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.8.

* gnu/packages/bioinformatics.scm (phylip): Delete variable.

Change-Id: I82382ccf745124889814d64ca95c2e8f9a4f671b
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

* gnu/packages/bioinformatics.scm (macs-3): Replace by an alias to...
(macs): ...this renamed package.
(python-peaks2utr)[propagated-inputs], (pigx-chipseq)[inputs]:
Replace macs-3 by macs.

Change-Id: Ib2c00a94ce9a2154f20ea0b58516207e4587f4c4