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| -rw-r--r-- | README.org (renamed from README.md) | 77 | ||||
| -rw-r--r-- | gn/deploy/machines.scm | 64 | ||||
| -rw-r--r-- | gn/deploy/machines/myserver.scm | 66 |
3 files changed, 161 insertions, 46 deletions
diff --git a/README.md b/README.org index 42712a0..1d51aaf 100644 --- a/README.md +++ b/README.org @@ -1,116 +1,101 @@ -# guix-bioinformatics +* guix-bioinformatics Bioinformatics packages for GNU Guix that are used in -http://genenetwork.org/. See -[Guix Notes](https://github.com/pjotrp/guix-notes/blob/master/HACKING.org) -for installing and hacking GNU Guix. +http://genenetwork.org/. See [[https://github.com/pjotrp/guix-notes/blob/master/HACKING.org][Guix notes]] for installing and hacking +GNU Guix. -To easily use the packages from this repo, simply add it to your `channels` list: +To easily use the packages from this repo, simply add it to your +`channels` list in ~/.config/guix/channels.scm as described +[[https://guix.gnu.org/manual/en/html_node/Channels.html][here]]: +#+BEGIN_SRC scheme (cons* (channel (name 'gn-bioinformatics) - (url "https://gitlab.com/genenetwork/guix-bioinformatics") + (url "https://git.genenetwork.org/pjotrp/guix-bioinformatics.git") (branch "master")) %default-channels) +#+END_SRC -and run `guix pull` like normal to update your software. This is the recommended -way to use the software from this repository and the code snippets in this -README assume you have done so. +and run `guix pull` like normal to update your software. This is the +recommended way to use the software from this repository and the code +snippets in this README assume you have done so. If you want to make changes to the packages in this repo then simply set the GUIX_PACKAGE_PATH to point to the root of this directory before running Guix. E.g. - git clone https://github.com/genenetwork/guix-bioinformatics.git +#+BEGIN_SRC bash + git clone https://git.genenetwork.org/pjotrp/guix-bioinformatics.git export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/ guix package -A cwl +#+END_SRC or using a checked out Guix repo with - env GUIX_PACKAGE_PATH=$genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -A cwl +: env GUIX_PACKAGE_PATH=$genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -A cwl Some (or most) of these package definitions should make it upstream into the GNU Guix repository when tested and stable. -## Slurm and munge +* Slurm and munge Install slurm with +#+BEGIN_SRC bash guix pull guix package -i slurm-llnl ~/.guix-profile/sbin/slurmd -C -D ClusterName=(null) NodeName=selinunte CPUs=4 Boards=1 SocketsPerBoard=1 CoresPerSocket=2 ThreadsPerCore=2 RealMemory=7890 TmpDisk=29909 +#+END_SRC -## Module system +* Module system Install the module environment with +#+BEGIN_SRC bash guix pull guix package -i environment-modules modulecmd --version VERSION=3.2.10 DATE=2012-12-21 +#+END_SRC -## python2-numarray 1.5.2 - -Install python2-numarray package with - - guix pull - guix package -i python2-numarray - -## Common Workflow Language (CWL) +* Common Workflow Language (CWL) Install the common workflow language tool cwltool with +#+BEGIN_SRC bash guix pull guix package -i python2-cwltool cwtool --version 1.0.20150916041152 +#+END_SRC -# Packages moved from here to main line GNU Guix - -## LLVM D compiler - -The LLVM D compiler was added to GNU Guix main stream! - - guix package -i ldc - -## Elixir and Erlang - -Both languages have gone in to main line Guix: - - guix package -i elixir - guix package -i erlang - -## R/qtl - -R-qtl is now part of main stream GNU Guix: - - guix package -i r-qtl r - -# Development tips +* Development tips -## Override individual packages +** Override individual packages The cheerful way of overriding a version of a package: +#+BEGIN_SRC scheme (use-modules (guix) (gnu packages emacs)) (package (inherit emacs) (name "emacs-snapshot") (source "/path/to/some-file-or-directory.tar.gz")) +#+END_SRC and then run: - guix package --install-from-file=that-file.scm +: guix package --install-from-file=that-file.scm -## LICENSE +* LICENSE These package descriptions (so-called Guix expressions) are distributed by the same license as GNU Guix, i.e. GPL3+ diff --git a/gn/deploy/machines.scm b/gn/deploy/machines.scm new file mode 100644 index 0000000..b54f2f1 --- /dev/null +++ b/gn/deploy/machines.scm @@ -0,0 +1,64 @@ +; Machine definitions + +(define-module (gn deploy machines) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix utils) + #:use-module (guix download) + #:use-module (guix gexp) + #:use-module (guix git-download) + #:use-module (guix build-system gnu) + #:use-module (guix build-system cmake) + #:use-module (guix build-system perl) + #:use-module (guix build-system python) + ;; #:use-module (guix build-system ruby) + #:use-module (guix build-system r) + #:use-module (guix build-system trivial) + #:use-module (gnu packages compression) + #:use-module (gnu packages web) + #:use-module (gn packages web) + #:use-module (srfi srfi-1)) + +; Configure a default version of the nginx web server +(define-public nginx-config + (let ((commit "e2ac61bfa472f23eb8e0c6863395a79c94a3d68a") + (revision "1")) + (package + (name "nginx-gn-config") + (version (git-version "0.0.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "http://git.genenetwork.org/pjotrp/guix-bioinformatics.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1pczs7farkcklvh96q1psjgv86mlwv93c3lzmc1mwp9m299g4qdr")))) + (build-system trivial-build-system) + (native-inputs `(("unzip" ,unzip) + ("source" ,source))) + (propagated-inputs `(("nginx" ,nginx))) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/etc/nginx")) + (nginx-etc (string-append (assoc-ref %build-inputs "nginx") + "/share/nginx/conf"))) + ; (write target) + (mkdir-p target) + ; copy original nginx configuration /gnu/store/nginx-ver/share/nginx/conf/* + ; (copy-recursively nginx-etc target) + (copy-file (string-append nginx-etc "/nginx.conf") + (string-append target "/nginx.conf")) + (plain-file "sudoers" "\ +root ALL=(ALL) ALL +%wheel ALL=(ALL) ALL\n") + #t)))) + (home-page "http://git.genenetwork.org/pjotrp/guix-bioinformatics") + (synopsis "Nginx configuration") + (description "None.") + (license license:expat)))) diff --git a/gn/deploy/machines/myserver.scm b/gn/deploy/machines/myserver.scm new file mode 100644 index 0000000..9a9923d --- /dev/null +++ b/gn/deploy/machines/myserver.scm @@ -0,0 +1,66 @@ +;; This is an operating system configuration template +;; for a "bare bones" setup, with no X11 display server. + +(use-modules (gnu) + (gnu packages web)) +(use-service-modules networking ssh web) +(use-package-modules screen ruby) + +(operating-system + (host-name "komputilo") + (timezone "Europe/Amsterdam") + (locale "en_US.utf8") + + ;; Boot in "legacy" BIOS mode, assuming /dev/sdX is the + ;; target hard disk, and "my-root" is the label of the target + ;; root file system. + (bootloader (bootloader-configuration + (bootloader grub-bootloader) + (target "/dev/sdX"))) + (file-systems (cons (file-system + (device (file-system-label "my-root")) + (mount-point "/") + (type "ext4")) + %base-file-systems)) + + ;; This is where user accounts are specified. The "root" + ;; account is implicit, and is initially created with the + ;; empty password. + (users (cons (user-account + (name "pjotr") + (password "$6$EoLVFsCpLywbQmy1$aJJ3dIrgIH4UtiTVynIZ0MiC667w4C5ybygGisUnUfusPrgxZ7ncz.Cjv67EJPA6VW3EPFbOaiadQzxFn2sLb.") + (comment "Pjotr") + (group "users") + + ;; Adding the account to the "wheel" group + ;; makes it a sudoer. Adding it to "audio" + ;; and "video" allows the user to play sound + ;; and access the webcam. + (supplementary-groups '("wheel" + "audio" "video"))) + %base-user-accounts)) + + ;; Globally-installed packages. + ; (packages (cons screen %base-packages)) + + (packages (append (list + screen nginx) + %base-packages)) + + + ;; Add services to the baseline: a DHCP client and + ;; an SSH server with nginx + (services (append (list (service dhcp-client-service-type) + (service openssh-service-type + (openssh-configuration + ; (authorized-keys + ; `(("pjotr" ,(local-file "/home/pjotr/.ssh/authorized_keys")))) + (password-authentication? #t) + (port-number 2222))) + (service nginx-service-type + (nginx-configuration + (server-blocks + (list (nginx-server-configuration + (listen '("8080"))))))) + ) + %base-services))) |