From c97646a5687f8ba834e3081bdee25a7457e90071 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 16 Dec 2019 05:12:23 -0600 Subject: Rename --- README.md | 97 -------------------------------------------------------------- README.org | 97 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 97 insertions(+), 97 deletions(-) delete mode 100644 README.md create mode 100644 README.org diff --git a/README.md b/README.md deleted file mode 100644 index 1132850..0000000 --- a/README.md +++ /dev/null @@ -1,97 +0,0 @@ -# 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. - -To easily use the packages from this repo, simply add it to your -`channels` list in ~/.config/guix/channels.scm as described -[here](https://guix.gnu.org/manual/en/html_node/Channels.html) - - (cons* - (channel - (name 'gn-bioinformatics) - (url "https://git.genenetwork.org/pjotrp/guix-bioinformatics.git") - (branch "master")) - %default-channels) - -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://git.genenetwork.org/pjotrp/guix-bioinformatics.git - export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/ - guix package -A cwl - -or using a checked out Guix repo with - - env GUIX_PACKAGE_PATH=$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 - -Install slurm with - - 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 - -## Module system - -Install the module environment with - - guix pull - guix package -i environment-modules - - modulecmd --version - VERSION=3.2.10 - DATE=2012-12-21 - -## python2-numarray 1.5.2 - -Install python2-numarray package with - - guix pull - guix package -i python2-numarray - -## Common Workflow Language (CWL) - -Install the common workflow language tool cwltool with - - guix pull - guix package -i python2-cwltool - - cwtool --version - 1.0.20150916041152 - -# Development tips - -## Override individual packages - -The cheerful way of overriding a version of a package: - - (use-modules (guix) (gnu packages emacs)) - - (package - (inherit emacs) - (name "emacs-snapshot") - (source "/path/to/some-file-or-directory.tar.gz")) - -and then run: - - guix package --install-from-file=that-file.scm - - -## LICENSE - -These package descriptions (so-called Guix expressions) are -distributed by the same license as GNU Guix, i.e. GPL3+ diff --git a/README.org b/README.org new file mode 100644 index 0000000..1132850 --- /dev/null +++ b/README.org @@ -0,0 +1,97 @@ +# 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. + +To easily use the packages from this repo, simply add it to your +`channels` list in ~/.config/guix/channels.scm as described +[here](https://guix.gnu.org/manual/en/html_node/Channels.html) + + (cons* + (channel + (name 'gn-bioinformatics) + (url "https://git.genenetwork.org/pjotrp/guix-bioinformatics.git") + (branch "master")) + %default-channels) + +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://git.genenetwork.org/pjotrp/guix-bioinformatics.git + export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/ + guix package -A cwl + +or using a checked out Guix repo with + + env GUIX_PACKAGE_PATH=$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 + +Install slurm with + + 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 + +## Module system + +Install the module environment with + + guix pull + guix package -i environment-modules + + modulecmd --version + VERSION=3.2.10 + DATE=2012-12-21 + +## python2-numarray 1.5.2 + +Install python2-numarray package with + + guix pull + guix package -i python2-numarray + +## Common Workflow Language (CWL) + +Install the common workflow language tool cwltool with + + guix pull + guix package -i python2-cwltool + + cwtool --version + 1.0.20150916041152 + +# Development tips + +## Override individual packages + +The cheerful way of overriding a version of a package: + + (use-modules (guix) (gnu packages emacs)) + + (package + (inherit emacs) + (name "emacs-snapshot") + (source "/path/to/some-file-or-directory.tar.gz")) + +and then run: + + guix package --install-from-file=that-file.scm + + +## LICENSE + +These package descriptions (so-called Guix expressions) are +distributed by the same license as GNU Guix, i.e. GPL3+ -- cgit v1.2.3