| Commit message (Collapse) | Author | Age |
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Conflicts:
gnu/packages/bioinformatics.scm
gnu/packages/cmake.scm
gnu/packages/curl.scm
gnu/packages/emacs-xyz.scm
gnu/packages/gpodder.scm
gnu/packages/music.scm
gnu/packages/patches/glibc-bootstrap-system.patch
gnu/packages/python-xyz.scm
gnu/packages/shells.scm
gnu/packages/statistics.scm
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* gnu/packages/bioinformatics.scm (seqan): Rename this variable...
(seqan-2): ...to this.
(seqan): New variable for seqan3.
(flexbar)[native-inputs]: Update name for seqan 2.
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* gnu/packages/bioinformatics.scm (segemehl): New variable.
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* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
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* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1.
[arguments]: Update custom 'check phase.
[propagated-inputs]: Replace htslib-1.9 with 1.10.
[native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10,
bcftools-1.9 with 1.10.
(bcftools-1.9): Replace with bcftools-1.10.
[native-inputs]: Replace htslib-1.9 with 1.10.
(samtools-1.9): Replace with samtools-1.10.
[inputs]: Replace htslib-1.9 with 1.10.
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* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
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* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
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* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
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* gnu/packages/bioinformatics.scm (r-ascat): New variable.
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* gnu/packages/bioinformatics.scm (nanosv): New variable.
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* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
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Renamed from python2-checkm-genome to checkm to better reflect its
status as standalone-application and support for Python 3.
* gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to…
(checkm): …here and update to 1.1.3.
[propagated-inputs]: Move to inputs.
[inputs]: Use Python 3 dependencies.
[home-page]: Point to real home-page.
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* gnu/packages/bioinformatics.scm (tombo): New variable.
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This changes some of the remaining uses of this idiom:
(string-append (assoc-ref inputs "LABEL") "FILE")
to one of:
(search-input-file inputs "FILE")
(search-input-directory inputs "FILE")
* gnu/packages/axoloti.scm (axoloti-patcher): Use
'search-input-directory'.
(axoloti-patcher-next): Likewise.
* gnu/packages/bioinformatics.scm (java-picard): Likewise.
* gnu/packages/bootloaders.scm (grub-hybrid): Likewise.
(u-boot-puma-rk3399): Likewise.
(u-boot-rock64-rk3328): Likewise.
(u-boot-firefly-rk3399): Likewise.
(u-boot-rockpro64-rk3399): Likewise.
(u-boot-pinebook-pro-rk3399): Likewise.
* gnu/packages/cran.scm (r-shiny): Likewise.
(r-shinytree): Likewise.
* gnu/packages/education.scm (anki): Likewise.
* gnu/packages/emacs-xyz.scm (emacs-flycheck-grammalecte): Likewise.
(emacs-rime): Likewise.
* gnu/packages/emulators.scm (dolphin-emu): Likewise.
* gnu/packages/games.scm (bsd-games): Likewise.
(seahorse-adventures): Likewise.
(einstein): Likewise.
* gnu/packages/gimp.scm (gimp-fourier): Likewise.
* gnu/packages/gnome.scm (gspell): Likewise.
* gnu/packages/guile-xyz.scm (guile-libyaml): Likewise.
* gnu/packages/java.scm (icedtea-7): Likewise.
* gnu/packages/language.scm (nimf): Likewise.
* gnu/packages/lxde.scm (spacefm): Likewise.
* gnu/packages/mail.scm (claws-mail): Likewise.
* gnu/packages/netpbm.scm (netpbm): Likewise.
* gnu/packages/networking.scm (blueman): Likewise.
* gnu/packages/scheme.scm (scm): Likewise.
* gnu/packages/security-token.scm (python-fido2): Likewise.
* gnu/packages/syndication.scm (rtv): Likewise.
* gnu/packages/tls.scm (acme-client): Likewise.
* gnu/packages/web.scm (netsurf): Likewise.
* gnu/packages/wine.scm (wine-staging): Likewise.
* gnu/packages/wxwidgets.scm (wxwidgets): Likewise.
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* gnu/packages/bioinformatics.scm (java-picard-1.113): Use
'search-input-file' when looking for *.jar.
(fastqc): Likewise.
* gnu/packages/groovy.scm (groovy): Likewise.
* gnu/packages/java.scm (ant-bootstrap): Likewise.
(ecj-bootstrap): Likewise.
(java-cisd-base): Likewise.
(java-cisd-args4j): Likewise.
(java-cisd-jhdf5): Likewise.
(java-native-access): Likewise.
(java-native-access-platform): Likewise.
* gnu/packages/maths.scm (hdf-java): Likewise.
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* gnu/packages/admin.scm (isc-dhcp): Use 'search-input-file' when
looking for executables.
* gnu/packages/audio.scm (ableton-link): Likewise.
* gnu/packages/benchmark.scm (fio): Likewise.
* gnu/packages/bioinformatics.scm (roary): Likewise.
(ngless): Likewise.
* gnu/packages/boost.scm (boost-for-irods): Likewise.
* gnu/packages/bootloaders.scm (grub): Likewise.
(grub-efi): Likewise.
* gnu/packages/chemistry.scm (inchi): Likewise.
* gnu/packages/dictionaries.scm (ding): Likewise.
* gnu/packages/dlang.scm (ldc): Likewise.
* gnu/packages/education.scm (childsplay): Likewise.
* gnu/packages/emacs-xyz.scm (emacs-hyperbole): Likewise.
(emacs-haskell-mode): Likewise.
(emacs-auctex): Likewise.
(emacs-ggtags): Likewise.
(emacs-graphviz-dot-mode): Likewise.
(emacs-flycheck-grammalecte): Likewise.
(emacs-counsel-notmuch): Likewise.
(emacspeak): Likewise.
(emacs-exwm): Likewise.
(emacs-exwm-x): Likewise.
(emacs-treemacs): Likewise.
(emacs-telega): Likewise.
(emacs-exiftool): Likewise.
* gnu/packages/emulators.scm (higan): Likewise.
* gnu/packages/engineering.scm (freehdl): Likewise.
(librepcb): Likewise.
* gnu/packages/entr.scm (entr): Likewise.
* gnu/packages/file-systems.scm (libeatmydata): Likewise.
(xfstests): Likewise.
(mergerfs): Likewise.
(mergerfs-tools): Likewise.
* gnu/packages/finance.scm (monero-gui): Likewise.
* gnu/packages/flashing-tools.scm (flashrom): Likewise.
* gnu/packages/fontutils.scm (fontforge): Likewise.
* gnu/packages/game-development.scm (python2-renpy): Likewise.
* gnu/packages/games.scm (opensurge): Likewise.
(xboard): Likewise.
(hyperrogue): Likewise.
(flare-game): Likewise.
(chessx): Likewise.
* gnu/packages/geo.scm (grass): Likewise.
* gnu/packages/glib.scm (glib): Likewise.
* gnu/packages/gnome.scm (mm-common): Likewise.
(network-manager-openvpn): Likewise.
(network-manager-vpnc): Likewise.
(network-manager-openconnect): Likewise.
(apostrophe): Likewise.
* gnu/packages/gnupg.scm (pius): Likewise.
(jetring): Likewise.
* gnu/packages/gnuzilla.scm (icedove): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
* gnu/packages/graphviz.scm (xdot): Likewise.
* gnu/packages/guile-xyz.scm (jupyter-guile-kernel): Likewise.
* gnu/packages/haskell-xyz.scm (ghc-hindent): Likewise.
* gnu/packages/ibus.scm (ibus): Likewise.
* gnu/packages/image.scm (phockup): Likewise.
* gnu/packages/irc.scm (quassel): Likewise.
* gnu/packages/java.scm (drip): Likewise.
(ant-bootstrap): Likewise.
(tla2tools): Likewise.
* gnu/packages/julia.scm (julia): Likewise.
* gnu/packages/less.scm (lesspipe): Likewise.
* gnu/packages/libreoffice.scm (libreoffice): Likewise.
* gnu/packages/linux.scm (fuse): Likewise.
(lm-sensors): Likewise.
(bluez): Likewise.
(fakeroot): Likewise.
(inputattach): Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-cl-diskspace): Likewise.
* gnu/packages/lisp.scm (lisp-repl-core-dumper): Likewise.
* gnu/packages/lua.scm (fennel): Likewise.
* gnu/packages/lxde.scm (spacefm): Likewise.
* gnu/packages/mail.scm (public-inbox): Likewise.
* gnu/packages/maths.scm (hdf-java): Likewise.
(maxima): Likewise.
(frama-c): Likewise.
* gnu/packages/messaging.scm (libgadu): Likewise.
* gnu/packages/music.scm (denemo): Likewise.
(curseradio): Likewise.
* gnu/packages/netpbm.scm (netpbm): Likewise.
* gnu/packages/networking.scm (blueman): Likewise.
(squid): Likewise.
(aircrack-ng): Likewise.
* gnu/packages/node.scm (node): Likewise.
(node-llparse-frontend-bootstrap): Likewise.
(node-llparse-bootstrap): Likewise.
(llhttp-bootstrap): Likewise.
(node-lts): Likewise.
* gnu/packages/ocaml.scm (ocaml-4.11): Likewise.
(opam): Likewise.
(ocaml-graph): Likewise.
* gnu/packages/orpheus.scm (orpheus): Likewise.
* gnu/packages/password-utils.scm (password-store): Likewise.
* gnu/packages/python.scm (pypy3): Likewise.
* gnu/packages/qt.scm (qt5ct): Likewise.
* gnu/packages/radio.scm (libosmo-dsp): Likewise.
* gnu/packages/ruby.scm (ruby-pandoc-ruby): Likewise.
* gnu/packages/rust.scm (rust-1.30): Likewise.
* gnu/packages/screen.scm (byobu): Likewise.
* gnu/packages/statistics.scm (r-with-tests): Likewise.
* gnu/packages/suckless.scm (surf): Likewise.
* gnu/packages/syndication.scm (gfeeds): Likewise.
* gnu/packages/telephony.scm (mumble): Likewise.
* gnu/packages/terminals.scm (alacritty): Likewise.
* gnu/packages/tex.scm (texlive-bin): Likewise.
* gnu/packages/uml.scm (plantuml): Likewise.
* gnu/packages/version-control.scm (python-git-multimail): Likewise.
(gitolite): Likewise.
(hg-commitsigs): Likewise.
(git-when-merged): Likewise.
(git-imerge): Likewise.
(gita): Likewise.
* gnu/packages/video.scm (you-get): Likewise.
* gnu/packages/vim.scm (eovim): Likewise.
* gnu/packages/virtualization.scm (qemu): Likewise.
(virt-manager): Likewise.
(criu): Likewise.
* gnu/packages/vpn.scm (strongswan): Likewise.
(xl2tpd): Likewise.
* gnu/packages/wm.scm (i3lock-fancy): Likewise.
* gnu/packages/wxwidgets.scm (python-wxpython): Likewise.
(python2-wxpython): Likewise.
* gnu/packages/xdisorg.scm (autorandr): Likewise.
* gnu/packages/xorg.scm (hackneyed-x11-cursors): Likewise.
(v86d): Likewise.
(mkfontdir): Likewise.
(xpra): Likewise.
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* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use
'search-input-file' when looking for *.a and *.so.
* gnu/packages/emulators.scm (dolphin-emu): Likewise.
* gnu/packages/engineering.scm (lepton-eda): Likewise.
(pcb): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
(go-1.14): Likewise.
* gnu/packages/haskell.scm (ghc-7): Likewise.
* gnu/packages/irods.scm (irods): Likewise.
* gnu/packages/language.scm (python2-tegaki-pygtk): Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-lzlib): Likewise.
(sbcl-cl-gobject-introspection): Likewise.
(sbcl-cl-ana): Likewise.
(sbcl-cl-libuv): Likewise.
(sbcl-cl-async): Likewise.
(sbcl-mcclim): Likewise.
(sbcl-zstd): Likewise.
(sbcl-cl-opengl): Likewise.
(sbcl-lev): Likewise.
(sbcl-cl-glfw3): Likewise.
* gnu/packages/machine-learning.scm (tensorflow): Likewise.
* gnu/packages/messaging.scm (utox): Likewise.
* gnu/packages/mpi.scm (java-openmpi): Likewise.
* gnu/packages/music.scm (jack-select): Likewise.
* gnu/packages/pascal.scm (fpc): Likewise.
* gnu/packages/python-crypto.scm (python-libnacl): Likewise.
* gnu/packages/python-xyz.scm (python-cairocffi): Likewise.
(python-pyev): Likewise.
(python-pytidylib): Likewise.
* gnu/packages/radio.scm (unixcw): Likewise.
* gnu/packages/rust.scm (rust-1.32): Likewise.
* gnu/packages/security-token.scm (opensc): Likewise.
(python-pyscard): Likewise.
* gnu/packages/selinux.scm (python-setools): Likewise.
* gnu/packages/spice.scm (libcacard): Likewise.
* gnu/packages/telephony.scm (libtgvoip): Likewise.
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* gnu/packages/arcan.scm (arcan)[arguments]: Use
'search-input-directory' for "include/libdrm" and "include/apr-1".
* gnu/packages/bioinformatics.scm (sailfish): Likewise for jellyfish.
* gnu/packages/boost.scm (boost-for-irods): Likewise for libcxx headers.
* gnu/packages/cedille.scm (cedille): Likewise for IAL headers.
* gnu/packages/compression.scm (snappy-with-clang6): Likewise for libcxx
headers.
* gnu/packages/cups.scm (hplip): Likewise for libusb headers.
* gnu/packages/emulators.scm (pcsxr): Likewise for libcdio headers.
* gnu/packages/game-development.scm (python2-renpy): Likewise for
fribidi headers.
* gnu/packages/games.scm (pokerth): Likewise for libircclient.
* gnu/packages/guile-xyz.scm (guile-persist): Likewise for Guile.
* gnu/packages/hurd.scm (hurd): Likewise for libtirpc.
* gnu/packages/irods.scm (irods, irods-client-icommands): Likewise for
libcxx, catch2, and nlohmann-json-cpp.
* gnu/packages/julia.scm (julia): Use 'search-input-file' for libuv's
errno.h.
* gnu/packages/kde-pim.scm (kdepim-runtime): Use
'search-input-directory' for "include/KF5".
(kmessagelib): Likewise.
* gnu/packages/kde.scm (kdeconnect): Likewise.
* gnu/packages/llvm.scm (clang-runtime-3.5): Likewise for libtirpc.
* gnu/packages/mpi.scm (openmpi): Likewise for "include/infiniband".
* gnu/packages/pumpio.scm (pumpa): Use 'search-input-file' for "tidy.h"
and "aspell.h".
* gnu/packages/radio.scm (dream): Use 'search-input-file' and
'search-input-directory' for pulseaudio, sndfile, etc.
* gnu/packages/selinux.scm (policycoreutils): Likewise for PAM and
libaudit.
* gnu/packages/serialization.scm (avro-cpp-1.9-for-irods): Likewise for
libcxx.
* gnu/packages/sync.scm (nextcloud-client): Likewise for "include/KF5".
* gnu/packages/video.scm (mkvtoolnix): Likewise for "include/gtest".
(libopenshot): Likewise for "include/UnitTest++".
* gnu/packages/virtualization.scm (criu): Likewise for libnl3 and for
protobuf file.
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* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use
'search-input-directory' when searching for Eigen headers.
* gnu/packages/bioinformatics.scm (nanopolish): Likewise.
* gnu/packages/machine-learning.scm (tensorflow): Likewise.
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* gnu/packages/backup.scm (duplicity)[arguments]: Use
'search-input-directory' for "share/zoneinfo".
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Likewise.
(pigx-bsseq): Likewise.
* gnu/packages/calcurse.scm (calcurse): Likewise.
* gnu/packages/calendar.scm (date): Likewise.
* gnu/packages/compression.scm (lhasa): Likewise.
* gnu/packages/cran.scm (r-rstan): Likewise.
* gnu/packages/django.scm (python-django): Likewise.
* gnu/packages/dlang.scm (ldc-bootstrap): Likewise.
* gnu/packages/finance.scm (ledger): Likewise.
* gnu/packages/glib.scm (glib): Likewise.
* gnu/packages/golang.scm (go-1.4): Likewise.
(go-1.14): Likewise.
* gnu/packages/kde-frameworks.scm (kcalendarcore): Likewise.
(kdelibs4support): Likewise.
* gnu/packages/kodi.scm (kodi): Likewise.
* gnu/packages/mail.scm (mu): Likewise.
* gnu/packages/perl.scm (perl-libtime-parsedate): Likewise.
* gnu/packages/python-xyz.scm (python-robotframework): Likewise.
(python-dparse): Likewise.
* gnu/packages/rrdtool.scm (rrdtool): Likewise.
* gnu/packages/statistics.scm (r-with-tests): Likewise.
* gnu/packages/vim.scm (vim): Likewise.
* gnu/packages/virtualization.scm (ganeti): Likewise.
* gnu/packages/vpn.scm (strongswan): Likewise.
* gnu/packages/xfce.scm (xfce4-panel): Likewise.
* gnu/packages/mate.scm (libmateweather): Use 'search-input-file' for
"share/zoneinfo/zone.tab".
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* gnu/packages/ocaml.scm (ocaml-sqlite3): New variable.
(ocaml4.07-sqlite3): Inherit from ocaml-sqlite3.
* gnu/packages/bioinformatics.scm (pplacer): Also use package-with-ocaml4.07
with ocaml-sqlite3.
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This could lead to circular reference breakage.
* gnu/packages/bioinformatics.scm (bioperl-minimal): Move top-level
references to perl-* variables and their transitive inputs to
'arguments' and 'inputs'.
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Line introduced in 4efbf56e5391dfbb3db3d6cee3138afaccb6cd64.
* gnu/packages/bioinformatics.scm: Remove unused (gnu packages
commencement) import.
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Conflicts:
gnu/packages/cups.scm
gnu/packages/python-web.scm
gnu/packages/web.scm
guix/build/maven/pom.scm
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* gnu/packages/bioinformatics.scm (ensembl-vep)[source]: Add a file-name
field.
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* gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
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* gnu/packages/bioinformatics.scm (python-iced): New variable.
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Note: this merge actually changes the 'curl' and 'python-attrs' derivations,
as part of solving caf4a7a2770ef4d05a6e18f40d602e51da749ddc and
12964df69a99de6190422c752fef65ef813f3b6b respectively.
4604d43c0e (gnu: gnutls@3.6.16: Fix cross-compilation.) was ignored because it
cannot currently be tested.
Conflicts:
gnu/local.mk
gnu/packages/aidc.scm
gnu/packages/boost.scm
gnu/packages/curl.scm
gnu/packages/nettle.scm
gnu/packages/networking.scm
gnu/packages/python-xyz.scm
gnu/packages/tls.scm
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* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
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This change was automated via the following command:
$ git ls-files | xargs sed -i 's/,qtbase)/,qtbase-5)/g'
$ git ls-files | xargs sed -i 's/inherit qtbase)/inherit qtbase-5)/g'
$ git ls-files | xargs sed -i 's/package-version qtbase)/package-version qtbase-5)/g'
$ git checkout etc # to clear some spurious changes
This is done so the qtbase package can be upgraded to version 6 in the
following commit.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.2.
[inputs]: Add wget.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.5.
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* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
[arguments]: Enabled tests. Remove 'relax-requirements phase.
[native-inputs]: Add python-pytest.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/python-xyz.scm (python-mappy): Move to ...
* gnu/packages/bioinformatics.scm: ... here.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.17.
[arguments]: Remove "use-latest-salmon" phase; add "set-timezone" phase.
[inputs]: Replace r-gprofiler with r-gprofiler2; add r-ggpubr and
python-deeptools.
[native-inputs]: Add tzdata.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase
"use-latest-salmon".
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* gnu/packages/bioinformatics.scm (salmon): Update to 1.4.0.
[arguments]: Remove unnecessary flags, add other soon-to-be-unnecessary flags;
remove "prepare-rapmap" phase, add "prepare-pufferfish" phase, add
"fix-error-message-in-tests" phase, simplify "use-system-libraries" phase.
[inputs]: Add curl and pufferfish sources; remove libdivsufsort and rapmap
sources.
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* gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
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* gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0.
[home-page]: Update to new home.
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* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.3.0.
[arguments]: Disable SSE to avoid tuning to the build node's CPU.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Update.
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* gnu/packages/bioinformatics.scm (multiqc): Update to 1.10.1.
[arguments]: Remove build phase "relax-requirements"; replace "check" phase.
[propagated-inputs]: Add python-coloredlogs, python-future, python-networkx,
and python-rich; remove python-nose.
[native-inputs]: Add python-pytest and the test suite.
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* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.
[source]: Download using git-fetch.
[arguments]: Enable tests. Add phase to make test data writable.
[propagated-inputs]: Add python-h5py, python-numpy, python-pandas,
python-scipy.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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Conflicts:
gnu/local.mk
gnu/packages/algebra.scm
gnu/packages/bioinformatics.scm
gnu/packages/curl.scm
gnu/packages/docbook.scm
gnu/packages/emacs-xyz.scm
gnu/packages/maths.scm
gnu/packages/plotutils.scm
gnu/packages/python-web.scm
gnu/packages/python-xyz.scm
gnu/packages/radio.scm
gnu/packages/readline.scm
gnu/packages/tls.scm
gnu/packages/xml.scm
gnu/packages/xorg.scm
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* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5.
[source]: Remove patch.
[arguments]: Adjust custom 'patch-source phase for changes in source.
[inputs]: Remove zlib.
* gnu/packages/patches/freebayes-devendor-deps.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
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* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11.
[arguments]: Add build phase "patch-tests"; replace "check" phase.
[native-inputs]: Add python-codecov, python-pytest-cov, and
python-pytest-flake8.
[propagated-inputs]: Add python-six and python-sparse.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13.
[arguments]: Remove obsolete substitutions.
[inputs]: Remove fastqc and trim-galore; add hisat2 and fastp.
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* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
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* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
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* gnu/packages/bioinformatics.scm (fit-sne): New variable.
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