gnu: Add seqtk. - guix - Wojtek's customized Guix

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author	Ben J Woodcroft <donttrustben@gmail.com>	2016-09-09 09:53:21 +1000
committer	Ben Woodcroft <donttrustben@gmail.com>	2016-09-13 20:27:29 +1000
commit	66daf78c0a4b64e0618a9bca8c8e6c0ce28de16d (patch)
tree	94ca5c467f0ac7ff549fd5d66a942a42146ce02d /emacs
parent	6c0cd765c03de72ecd97b9222bff04c525b8bba4 (diff)
download	guix-66daf78c0a4b64e0618a9bca8c8e6c0ce28de16d.tar.gz guix-66daf78c0a4b64e0618a9bca8c8e6c0ce28de16d.zip

gnu: Add seqtk.

* gnu/packages/bioinformatics.scm (seqtk): New variable.

Diffstat (limited to 'emacs')

0 files changed, 0 insertions, 0 deletions

: Add (guix build bournish). * gnu/services/base.scm (file-system-shepherd-service)[imported-modules]: Likewise. * gnu/system/linux-container.scm (container-script): Likewise. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Likewise. 2016-01-01system: Allow the root file system to have a UUID.Ludovic Courtès This is a followup to ab64483. * gnu/system.scm (mapped-device-user): Check whether the title of FS is 'device before calling 'string=?'. * gnu/system/vm.scm (virtualized-operating-system)[user-file-systems]: Likewise. 2015-11-21gnu: Add qemu-minimal.Ludovic Courtès * gnu/packages/qemu.scm (qemu): Exchange with former QEMU-HEADLESS. (qemu-headless): Rename to... (qemu-minimal): ... this. New variable. Pass --target-list. * gnu/packages/debug.scm (qemu-2.3.0): Inherit from QEMU-MINIMAL. * gnu/packages/grub.scm (qemu-for-tests): Likewise. * gnu/system/vm.scm (expression->derivation-in-linux-vm, qemu-image): Update to name change. 2015-11-03system: Rename (gnu system linux) to (gnu system pam).Ludovic Courtès * gnu/system/linux.scm: Rename to... * gnu/system/pam.scm: ... this. * gnu-system.am (GNU_SYSTEM_MODULES): Adjust accordingly. * gnu.scm, gnu/services/base.scm, gnu/services/desktop.scm, gnu/services/networking.scm, gnu/services/ssh.scm, gnu/services/xorg.scm, gnu/system.scm, gnu/system/vm.scm: Likewise. 2015-07-26vm: Make the list of partitions to build a parameter.Ludovic Courtès * gnu/build/vm.scm (<partition>): New record type. (fold2): New procedure. (initialize-partition-table): Remove #:bootable? and 'partition-size' parameters. Add 'partitions' parameter. Invoke 'parted' with '--script'. (initialize-root-partition): Remove. (initialize-partition, root-partition-initializer): New procedures. (initialize-hard-disk): Remove #:system-directory, #:disk-image-size, #:file-system-type, #:file-system-label, #:closures, #:copy-closures?, #:bootable?, and #:register-closures? parameters. Add #:partitions. Rewrite to use 'initialize-partition' for each item of PARTITIONS. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Add (guix records) to #:modules default value. (qemu-image): Adjust accordingly. 2015-07-24vm: Use the 'umount' procedure instead of util-linux's 'umount' command.Ludovic Courtès * gnu/build/vm.scm (initialize-root-partition, initialize-hard-disk): Use the 'umount' procedure instead of invoking the 'umount' command. * gnu/system/vm.scm (qemu-image): Remove UTIL-LINUX from INPUTS. 2015-07-17system: Add 'kernel-arguments' field.Ludovic Courtès * gnu/system.scm (<operating-system>)[kernel-arguments]: New field. (operating-system-grub.cfg): Honor it. (operating-system-parameters-file): Add 'kernel-arguments' to the parameters file. * guix/scripts/system.scm (previous-grub-entries)[system->grub-entry]: Read the 'kernel-arguments' field of the parameters file, when available. * gnu/system/vm.scm (system-qemu-image/shared-store-script): Use (operating-system-kernel-arguments os) in '-append'. * doc/guix.texi (operating-system Reference): Document it. 2015-07-10gnu: Include (guix build syscalls) module in initrd/VM derivations.David Thompson This bug was introduced in commit 85c3127. Thanks to Christopher Webber for reporting it. * gnu/syste/linux-initrd.scm (base-initrd): Include (guix build syscalls) module in derivation. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Likewise. 2015-07-07gnu: system: Move <file-system-mapping> into (gnu system file-systems).David Thompson * gnu/system/vm.scm (<file-system-mapping>, %store-mapping): Move from here... * gnu/system/file-systems.scm: ...to here. * guix/scripts/system.scm: Import (gnu system file-systems). 2015-04-05system: Take kernel modules from the user-specified kernel.Andy Wingo * gnu/system/linux-initrd.scm (base-initrd): Add #:linux option to specify the linux kernel to use. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Propagate #:linux to base-initrd. * gnu/system.scm (operating-system-initrd-file): Pass #:linux to 'make-initrd'. Co-authored-by: Ludovic Courtès <ludo@gnu.org> 2015-01-27linux-initrd: Add USB kernel modules to the default initrd.Ludovic Courtès * gnu/system/linux-initrd.scm (base-initrd)[linux-modules]: Add usb-storage, uas, usbkbd, and usbhid. * gnu/system/vm.scm (system-disk-image): Remove #:extra-modules argument to 'base-initrd'. 2014-12-13vm: Use QEMU's standard VGA emulation by default.Ludovic Courtès * gnu/system/vm.scm (common-qemu-options): Add "-vga std". 2014-11-28linux-boot: Load modules and their dependencies, à la 'modprobe'.Ludovic Courtès * gnu/build/linux-boot.scm: Use (gnu build linux-modules). (load-linux-module*): Remove. (boot-system): Add #:linux-module-directory parameter. [lookup-module]: New procedure. Call 'current-module-debugging-port'. Pass #:lookup-module to 'load-linux-module*'. Map LOOKUP-MODULE on LINUX-MODULES. * gnu/system/linux-initrd.scm (base-initrd): Adjust 'boot-system' call accordingly. Adjust #:modules argument as well. * gnu/system.scm (operating-system-activation-script)[%modules]: Likewise. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Likewise. 2014-11-20vm: Introduce 'file-system-mapping'.Ludovic Courtès * gnu/system/vm.scm (<file-system-mapping>): New record type. (%store-mapping): New variable. (host-9p-file-system): Rename to... (mapping->file-system): ... this. Replace 'source' and 'target' parameters with 'mapping'. Set 'flags' field. (virtualized-operating-system): Add 'mappings' parameter and honor it. (system-qemu-image/shared-store-script): Add 'mappings' parameter. Pass it to 'virtualized-operating-system'. Use it in argument to 'common-qemu-options'. 2014-11-20vm: Formalize use of '-virtfs' options.Ludovic Courtès * gnu/system/vm.scm (file-system->mount-tag, host-9p-file-system): New procedures. (virtualized-operating-system): Use 'host-9p-file-system' for the store. (common-qemu-options): Add 'shared-fs' parameter. [virtfs-option]: New procedure. Use it. (system-qemu-image/shared-store-script): Adjust accordingly. 2014-11-08vm: The 'run-vm' scripts now passes its arguments to QEMU.Ludovic Courtès * gnu/system/vm.scm (system-qemu-image/shared-store-script): Add "$@" at the end of the script. (common-qemu-options): Remove trailing newline. * doc/guix.texi (Invoking guix system): Document it. 2014-11-08vm: Fix 'vm --full-boot' to produce a sufficient disk image.Ludovic Courtès * gnu/system/vm.scm (system-qemu-image/shared-store): Add #:disk-image-size and #:full-boot? parameters and honor them. Pass '#:copy-inputs? full-boot?', and change #:inputs argument. * guix/scripts/system.scm (system-derivation-for-action): Pass #:disk-image-size to 'system-qemu-image/shared-store'. * doc/guix.texi (Invoking guix system): Mention use of '--image-size' in conjunction with '--full-boot'. 2014-11-08vm: Support 'guix system vm --full-boot'.Ludovic Courtès * gnu/system/vm.scm (system-qemu-image/shared-store-script): Add #:full-boot? parameter and honor it. * guix/scripts/system.scm (system-derivation-for-action): Likewise. (perform-action): Likewise. (show-help): Document '--full-boot'. (%options): Add '--full-boot'. (guix-system): Add #:full-boot? argument in call to 'perform-action'. * doc/guix.texi (Invoking guix system): Document it. 2014-11-06vm: Factorize common QEMU options.Ludovic Courtès * gnu/system/vm.scm (common-qemu-options): New procedure. (system-qemu-image/shared-store-script): Use it. 2014-11-06vm: Remove unused procedure.Ludovic Courtès * gnu/system/vm.scm (input->name+output): Remove. Its last user disappeared in commit b53833b. 2014-11-05vm: Disable swap devices in virtualized OSes.Ludovic Courtès * gnu/system/vm.scm (virtualized-operating-system): Add 'swap-devices' field. 2014-09-22linux-initrd: Adjust VM code and doc to new 'base-initrd' signature.Ludovic Courtès This fixes regressions introduced in de1c158 ("system: Add support for boot-time mapped devices."). * doc/guix.texi (Initial RAM Disk): Adjust example with custom use of 'base-initrd'. Document #:mapped-devices parameter of 'base-initrd'. * gnu/system/vm.scm (system-disk-image, system-qemu-image, virtualized-operating-system): Adjust call to 'base-initrd' to new signature. 2014-09-18linux-initrd: Remove now obsolete #:guile-modules-in-chroot? parameter.Ludovic Courtès * gnu/build/linux-boot.scm (boot-system): Remove #:guile-modules-in-chroot? and related code. * gnu/system/linux-initrd.scm (base-initrd): Likewise. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Remove #:guile-modules-in-chroot? argument in 'base-initrd' call. 2014-09-08linux-initrd: Copy all the script's closure to the initrd.Ludovic Courtès * gnu/system/linux-initrd.scm (expression->initrd): Remove calls to 'imported-modules' and 'compiled-modules'. Use 'gexp->script' with EXP. Add the result to TO-COPY. Make /init a symlink to that script, and copy its closure into the "contents" directory. Add fake /proc/self/exe symlink. * gnu/build/linux-boot.scm (load-linux-module*): Add comment about mmap. * gnu/system/vm.scm (system-qemu-image/shared-store-script): Add "-m 256". This turns out to be needed for initrds containing things like e2fsck and several modules; with the default of 128 MiB, loading libahci.ko may fail with -1. 2014-09-06gexp: Allow use of high-level objects in #:references-graphs.Ludovic Courtès * guix/gexp.scm (lower-reference-graphs): New procedure. (gexp->derivation)[graphs-file-names]: New procedure. Use 'lower-reference-graphs', and augment #:inputs argument as a function of #:references-graphs. * doc/guix.texi (G-Expressions): Adjust 'gexp->derivation' documentation accordingly. * tests/gexp.scm ("gexp->derivation, store copy"): Remove reference to TWO in BUILD-DRV. Use TWO directly in #:references-graphs argument. ("gexp->derivation #:references-graphs"): New test. * gnu/system/vm.scm (qemu-image): Remove variable 'graph'; use INPUTS as the #:references-graphs argument to 'expression->derivation-in-linux-vm'. 2014-09-04vm: Move store copy handling to (guix build store-copy).Ludovic Courtès * gnu/build/vm.scm (read-reference-graph, populate-store): Move to... * guix/build/store-copy.scm: ... here. New file. * Makefile.am (MODULES): Add it. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Adjust default #:modules values accordingly. * tests/gexp.scm ("gexp->derivation, store copy"): New test. 2014-09-03Move part of (gnu build linux-boot) to (gnu build file-systems).Ludovic Courtès * gnu/build/linux-boot.scm (%ext2-endianness, %ext2-sblock-magic, %ext2-sblock-creator-os, %ext2-sblock-uuid, %ext2-sblock-volume-name, read-ext2-superblock, ext2-superblock-uuid, ext2-superblock-volume-name, disk-partitions, partition-label-predicate, find-partition-by-label, canonicalize-device-spec, MS_RDONLY, MS_NOSUID, MS_NODEV, MS_NOEXEC, MS_BIND, MS_MOVE, bind-mount, check-file-system, mount-flags->bit-mask, mount-file-system): Move to... * gnu/build/file-systems.scm: ... here. New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it. * gnu/services/base.scm: Use (gnu build file-systems). * gnu/services/dmd.scm (dmd-configuration-file): Likewise. * gnu/system.scm (operating-system-activation-script): Likewise. * gnu/system/linux-initrd.scm (base-initrd): Likewise. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Likewise. 2014-09-03Rename (gnu build linux-initrd) to (gnu build linux-boot).Ludovic Courtès * gnu/build/linux-initrd.scm: Rename to... * gnu/build/linux-boot.scm: ... this. * gnu-system.am (GNU_SYSTEM_MODULES): Adjust accordingly. * gnu/build/activation.scm, gnu/build/vm.scm, gnu/services/base.scm, gnu/services/dmd.scm, gnu/system.scm, gnu/system/linux-initrd.scm, gnu/system/vm.scm: Adjust accordingly. 2014-09-03Move operating system helpers from (guix build …) to (gnu build …).Ludovic Courtès * guix/build/activation.scm, guix/build/install.scm, guix/build/linux-initrd.scm, guix/build/vm.scm: Move to... * gnu/build: ... here. * Makefile.am (MODULES): Remove the above guix/build/ files. * gnu-system.am (GNU_SYSTEM_MODULES): Add the above gnu/build/ files here. * gnu/services/base.scm, gnu/services/dmd.scm, gnu/system.scm, gnu/system/linux-initrd.scm, gnu/system/vm.scm, guix/scripts/system.scm: Adjust to the new module names. 2014-08-28gnu: Split (gnu packages base), adding (gnu packages commencement).Ludovic Courtès * gnu/packages/base.scm (gnu-make-boot0, diffutils-boot0, findutils-boot0, %boot0-inputs, nix-system->gnu-triplet, boot-triplet, binutils-boot0, gcc-boot0, perl-boot0, linux-libre-headers-boot0, texinfo-boot0, %boot1-inputs, glibc-final-with-bootstrap-bash, cross-gcc-wrapper, static-bash-for-glibc, glibc-final, gcc-boot0-wrapped, %boot2-inputs, binutils-final, libstdc++, gcc-final, ld-wrapper-boot3, %boot3-inputs, bash-final, %boot4-inputs, guile-final, gnu-make-final, ld-wrapper, coreutils-final, grep-final, %boot5-inputs, %final-inputs, canonical-package, gcc-toolchain, gcc-toolchain-4.8, gcc-toolchain-4.9): Move to... * gnu/packages/commencement.scm: ... here. New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it. * build-aux/check-final-inputs-self-contained.scm: Adjust accordingly. * gnu/packages/cross-base.scm: Likewise. * gnu/packages/make-bootstrap.scm: Likewise. * guix/build-system/cmake.scm (cmake-build): Likewise. * guix/build-system/gnu.scm (standard-packages, gnu-build, gnu-cross-build): Likewise. * guix/build-system/perl.scm (perl-build): Likewise. * guix/build-system/python.scm (python-build): Likewise. * guix/build-system/trivial.scm (guile-for-build): Likewise. * guix/download.scm (url-fetch): Likewise. * guix/gexp.scm (default-guile): Likewise. * guix/git-download.scm (git-fetch): Likewise. * guix/monads.scm (run-with-store): Likewise. * guix/packages.scm (default-guile): Likewise. * guix/scripts/package.scm (guix-package): Likewise. * guix/scripts/refresh.scm: Likewise. * guix/svn-download.scm (svn-fetch): Likewise. * tests/builders.scm (%bootstrap-inputs, %bootstrap-search-paths): Likewise. * tests/packages.scm ("GNU Make, bootstrap"): Likewise. * tests/guix-package.sh: Likewise. * gnu/services/base.scm: Use 'canonical-package' instead of xxx-final. * gnu/services/xorg.scm: Likewise. * gnu/system/vm.scm: Likewise. * guix/scripts/pull.scm (guix-pull): Likewise. 2014-07-14vm: Make sure disk image initrds load 'usb-storage.ko'.Ludovic Courtès Reported by David Thompson <dthompson2@worcester.edu>. * gnu/system/vm.scm (system-disk-image): Add usb-storage.ko to the initrd. 2014-07-13vm: Add support for i686.Ludovic Courtès Partially fixes <http://bugs.gnu.org/18002>. Reported by David Thompson <dthompson2@worcester.edu>. * guix/build/vm.scm (qemu-command): Add optional 'system' parameter. Special-case "^i[3456]86$". * gnu/system/vm.scm (system-qemu-image/shared-store-script): Use it.


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