guix-bioinformatics/guix - guix

Commit Graph

Author	SHA1	Message	Date
Ludovic Courtès	6750877f46	git-download: Support recursive clones. * guix/git-download.scm (<git-reference>)[recursive?]: New field. (git-fetch): Add 'inputs' variable. Add it to the #:inputs argument of 'build-expression->derivation'. Augment builder with call to 'set-path-environment-variable', and pass #:recursive? to 'git-fetch'. * guix/build/git.scm (git-fetch): Add #:recursive? parameter. Pass --recursive when RECURSIVE? is true, and delete all the '.git' files.	8 years ago
Ludovic Courtès	20b1d19e10	gnu: Adjust for (gnu packages image) merger. * gnu/packages/aidc.scm: Use (gnu packages image).	8 years ago
Ludovic Courtès	459dd9eaf2	system: Add a 'system?' field to user accounts. * gnu/system/shadow.scm (<user-account>)[system?]: New field. * gnu/system.scm (user-account->gexp): Add it. * guix/build/activation.scm (add-user): Add #:system? parameter and honor it. (activate-users+groups): Handle the 'system?' part of user tuples. Pass it to 'add-user'. Don't create PROFILE-DIR when SYSTEM? is true. * gnu/services/dbus.scm (dbus-service): Add 'system?' field for "messagebus" account. * gnu/services/base.scm (guix-build-accounts): Likewise. * gnu/services/avahi.scm (avahi-service): Likewise.	8 years ago
Ludovic Courtès	f2c403eab6	system: Install /var/guix/profiles/system-1-link on new systems. * guix/build/install.scm (directives): Add /var/guix/profiles/system. (populate-root-file-system): Add 'system' parameter. Create /var/guix/profiles/system-1-link. * guix/scripts/system.scm (install): Pass OS-DIR to 'populate-root-file-system'. * guix/build/vm.scm (initialize-root-partition): Add #:system-directory parameter, and pass it to 'populate-root-file-system'. (initialize-hard-disk): Add #:system-directory parameter, and pass it to 'initialize-root-partition'. * gnu/system/vm.scm (qemu-image): Add #:os-derivation parameter and pass it to 'initialize-hard-disk'. (system-disk-image, system-qemu-image, system-qemu-image/shared-store): Pass #:os-derivation to 'qemu-image.	8 years ago
John Darrington	dff624230a	gnu: Add talkfilters. * gnu/packages/games.scm (talkfilters): New variable.	8 years ago
John Darrington	51d3dcea42	gnu: Add qrencode. * gnu/packages/aidc.scm (qrencode): New variable.	8 years ago
David Thompson	e55354b87e	gnu: Consolidate libjpeg, libpng, and libtiff into one module. * gnu/packages/image.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add image.scm and remove libjpeg.scm, libpng.scm, and libtiff.scm. * gnu/packages/libjpeg.scm, gnu/packages/libpng.scm, gnu/packages/libtiff.scm: Delete files. * gnu/packages/emacs.scm gnu/packages/games.scm, gnu/packages/gd.scm, gnu/packages/geeqie.scm, gnu/packages/ghostscript.scm, gnu/packages/gimp.scm, gnu/packages/gnome.scm, gnu/packages/gnunet.scm, gnu/packages/gnustep.scm, gnu/packages/gnuzilla.scm, gnu/packages/graphviz.scm, gnu/packages/gtk.scm, gnu/packages/imagemagick.scm, gnu/packages/inkscape.scm, gnu/packages/netpbm.scm, gnu/packages/pdf.scm, gnu/packages/plotutils.scm, gnu/packages/qemu.scm, gnu/packages/qt.scm, gnu/packages/scheme.scm, gnu/packages/sdl.scm, gnu/packages/slim.scm, gnu/packages/tcl.scm, gnu/packages/texlive.scm, gnu/packages/video.scm, gnu/packages/xiph.scm, gnu/packages/xorg.scm: Use (gnu packages image) module.	8 years ago
David Thompson	dc55b8b234	gnu: Enable libvpx support in ffmpeg. * gnu/packages/video.scm (ffmpeg): Add libvpx input.	8 years ago
Ludovic Courtès	8a6d273137	system: Adjust the set of fields with default values. * gnu/system.scm (<operating-system>)[file-systems]: Remove default. [locale]: Add default value.	8 years ago
Ludovic Courtès	b25937e318	guix system: Add 'reconfigure' action. * guix/scripts/system.scm (%system-profile): New variable. (switch-to-system, previous-grub-entries): New procedures. (unless-file-not-found): New macro. (show-help): Add 'reconfigure'. (guix-system): Handle it. * gnu/system.scm: Export 'operating-system-activation-script'. * doc/guix.texi (Invoking guix system): Document it.	8 years ago
Ludovic Courtès	f01efec09a	activation: Preserve /etc/groups upon reboots. This is a followup to `e2fcc23`. The /etc/group file would be cleared when booting. * guix/build/activation.scm (activate-users+groups)[touch]: Rewrite so it does not wipe out FILE's contents.	8 years ago
Ludovic Courtès	c1202fb1f9	guix {system,offload}: Improve reporting of syntax errors. * guix/scripts/system.scm (read-operating-system) <catch handler>: Add case for 'syntax-error'. Correct message for default case. * guix/scripts/offload.scm (build-machines) <catch handler>: Add case for 'syntax-error'. * tests/guix-system.sh: New file. * Makefile.am (SH_TESTS): Add it.	8 years ago
David Thompson	80b77646a4	gnu: Add libsodium. * gnu-system.am (GNU_SYSTEM_MODULES): Add crypto.scm. * gnu/packages/crypto.scm: New file.	8 years ago
David Thompson	7025a035df	gnu: Add guile-opengl. * gnu/packages/gl.scm (guile-opengl): New variable.	8 years ago
David Thompson	d0ed39be55	gnu: Add libvpx. * gnu/packages/video.scm (libvpx): New variable.	8 years ago
John Darrington	091befba64	gnu: Add new package barcode * gnu/packages/aidc.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it.	8 years ago
Ludovic Courtès	fe6e3fe2a5	system: Support the addition of old entries in the GRUB menu. * gnu/system.scm (operating-system-grub.cfg): Add 'old-entries' parameter. Pass it to 'grub-configuration-file'. * gnu/system/grub.scm (grub-configuration-file): Add #:old-entries parameter. Honor it.	8 years ago
Ludovic Courtès	64e40dbb69	system: Store boot parameters in the system derivation. * gnu/system.scm (operating-system-parameters-file): New procedure. (operating-system-derivation): Use it to produce a 'parameters' files.	8 years ago
Ludovic Courtès	2d23e6f051	system: Factorize GRUB menu entry label. * gnu/system.scm (kernel->grub-label): New procedure. (operating-system-grub.cfg): Use it.	8 years ago
Eric Bavier	7cd157e221	gnu: cursynth: Upgrade to 1.5. * gnu/packages/cursynth.scm (cursynth)[source]: Upgrade to 1.5. New 'patches' field. * gnu/packages/patches/cursynth-wave-rand.patch: New patch. * gnu-system.am (dist_patch_DATA): Add it.	8 years ago
Ludovic Courtès	edc28d3c42	gnu: libmicrohttpd: Upgrade to 0.9.37. * gnu/packages/gnunet.scm (libmicrohttpd): Upgrade to 0.9.37.	8 years ago
Ludovic Courtès	58970d6a5d	gnu: gnupg: Upgrade versions 1 and 2 (security fix.) * gnu/packages/gnupg.scm (gnupg): Upgrade to 2.0.24. (gnupg-1): Upgrade to 1.4.17.	8 years ago
Ludovic Courtès	473dad6fde	gnu: libgpg-error: Upgrade to 1.13. * gnu/packages/gnupg.scm (libgpg-error): Upgrade to 1.13.	8 years ago
Ludovic Courtès	7f27b32f31	gnu: nano: Upgrade to 2.3.4. * gnu/packages/nano.scm (nano): Upgrade to 2.3.4.	8 years ago
Ludovic Courtès	0179cd7ed2	gnu: lightning: Upgrade to 2.0.4. * gnu/packages/lightning.scm (lightning): Upgrade to 2.0.4.	8 years ago
Ludovic Courtès	85f35ad623	gnu: ddrescue: Upgrade to 1.18.1. * gnu/packages/disk.scm (ddrescue): Upgrade to 1.18.1.	8 years ago
Ludovic Courtès	d12c626cf8	gnu: mcron: Upgrade to 1.0.8. * gnu/packages/guile.scm (mcron): Upgrade to 1.0.8.	8 years ago
Ludovic Courtès	5177f0fb41	gnu: libtasn1: Upgrade to 3.6. * gnu/packages/gnutls.scm (libtasn1): Upgrade to 3.6.	8 years ago
Ludovic Courtès	39ed6749dd	gnu: nettle: Add version 3.0. * gnu/packages/nettle.scm (nettle-3): New variable.	8 years ago
Eric Bavier	b4eab6a6a5	gnu: parallel: Upgrade to 20140622. * gnu/packages/parallel.scm (parallel)[source]: Upgrade to 20140622.	8 years ago
Eric Bavier	f4bf37825b	gnu: moe: Upgrade to 1.6. * gnu/packages/moe.scm (moe)[source]: Upgrade to 1.6. Add 'native-inputs' field.	8 years ago
Ludovic Courtès	cadf6cb4cf	guix system: Gracefully handle 'install-grub' errors. * guix/scripts/system.scm (install): Wrap 'install-grub' call in 'false-if-exception'. This is a followup to `641f9a2a`.	8 years ago
Ludovic Courtès	f6ad09ae5a	gnu: Move JSON-C to (gnu packages web). * gnu/packages/pulseaudio.scm (json-c): Move to... * gnu/packages/web.scm (json-c): ... here. New variable.	8 years ago
Ludovic Courtès	9ab7415329	gnu: json-c: Upgrade to 0.12. * gnu/packages/pulseaudio.scm (json-c)[source]: Upgrade to 0.12. Add 'modules' and 'snippet' fields.	8 years ago
Ludovic Courtès	e11390df55	install: Use udev. * gnu/system/install.scm (installation-services): Call 'udev-service'.	8 years ago
Ludovic Courtès	151a2c07aa	services: Add udev service, and add it to '%base-services'. * gnu/services/base.scm (udev-service): New procedure. (%base-services): Use it. * gnu/system.scm (%base-packages): Add UDEV.	8 years ago
David Thompson	1bd3f84986	gnu: Add notmuch. * gnu/packages/mail.scm (notmuch): New variable.	8 years ago
David Thompson	f4eae897cb	gnu: Add dtach. gnu/packages/screen.scm (dtach): New variable.	8 years ago
David Thompson	1790739c75	gnu: Add talloc. * gnu/packages/samba.scm (talloc): New variable.	8 years ago
Ludovic Courtès	b76a384715	system: Use the default 'groups' field. * gnu/system/install.scm (installation-os): Remove 'groups' field. * build-aux/hydra/demo-os.scm: Likewise.	8 years ago
Ludovic Courtès	773e956d5d	system: Augment the default set of groups. * gnu/system/shadow.scm (%base-groups): New variable. * gnu/system.scm (<operating-system>)[groups]: Use it as the default.	8 years ago
Ludovic Courtès	72507e23b5	system: Remove useless 'members' field of 'user-group'. * gnu/system/shadow.scm (<user-group>)[members]: Remove field. * gnu/system/install.scm (installation-os)[users]: Remove 'members' fields. Use 'supplementary-groups' for 'guest'. * build-aux/hydra/demo-os.scm (users): Likewise. * gnu/services/base.scm (guix-service): Remove 'members' field.	8 years ago
Ludovic Courtès	528b6a3dce	gnu: kmod: Honor $LINUX_MODULE_DIRECTORY. * gnu/packages/patches/kmod-module-directory.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/linux.scm (kmod)[origin]: Use it.	8 years ago
Andreas Enge	d7d42d6b24	gnu: Add udev. * gnu/packages/linux.scm (udev): New variable. * gnu/packages/patches/udev-gir-libtool.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. Co-authored-by: Ludovic Courtès <ludo@gnu.org>	8 years ago
Andreas Enge	e062d54240	gnu: Add kmod. * gnu/packages/linux.scm (kmod): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>	8 years ago
Ludovic Courtès	9b9148d8bb	linux-initrd: Allow unionfs to have a large number of open files. Fixes <http://bugs.gnu.org/17827>. * guix/build/linux-initrd.scm (mount-root-file-system) [volatile-root?]: Pass unionfs '-o max_file=65536'.	8 years ago
Ludovic Courtès	738146bfd4	nls: Update 'sr' translation.	8 years ago
Ludovic Courtès	b6a4dba116	gnu: man-pages: Upgrade to 3.69. * gnu/packages/man.scm (man-pages): Upgrade to 3.69.	8 years ago
Ludovic Courtès	d3e3b77dcc	gnu: gnupg: Upgrade to 2.0.23. * gnu/packages/gnupg.scm (gnupg): Upgrade to 2.0.23.	8 years ago
Ludovic Courtès	ea9711018c	gnu: global: Upgrade to 6.3. * gnu/packages/global.scm (global): Upgrade to 6.3.	8 years ago

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3258 Commits (6750877f46e684688075674c6e342895a24a52c9) All Branches Search

3258 Commits (6750877f46e684688075674c6e342895a24a52c9)

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