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diff --git a/doc/README.org b/doc/README.org index 43c92e3c..1236016e 100644 --- a/doc/README.org +++ b/doc/README.org @@ -2,7 +2,9 @@ * Table of Contents :TOC: - [[#introduction][Introduction]] - - [[#install][Install]] + - [[#check-list][Check list]] + - [[#installing-guix-packages][Installing Guix packages]] + - [[#creating-a-gnu-guix-profile][Creating a GNU Guix profile]] - [[#running-gn2][Running GN2]] - [[#run-gn-proxy][Run gn-proxy]] - [[#run-redis][Run Redis]] @@ -37,32 +39,106 @@ tree. Current supported versions can be found as the SHA values of For a full view of runtime dependencies as defined by GNU Guix, see an example of the [[#gn2-dependency-graph][GN2 Dependency Graph]]. -* Install +* Check list + +To run GeneNetwork the following services need to function: + +1. [ ] GNU Guix with a guix profile for genenetwork2 +1. [ ] A path to the (static) genotype files +1. [ ] Gn-proxy for authentication +1. [ ] The genenetwork3 service +1. [ ] Redis +1. [ ] Mariadb + +* Installing Guix packages Make sure to install GNU Guix using the binary download instructions on the main website. Follow the instructions on [[GUIX-Reproducible-from-source.org]] to download pre-built binaries. Note -the download amounts to several GBs of data. +the download amounts to several GBs of data. Debian-derived distros +may support + +: apt-get install guix + +* Creating a GNU Guix profile + +We run a GNU Guix channel with packages at [[https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics][guix-bioinformatics]]. The +README has instructions for hosting a channel, but typically we use +the GUIX_PACKAGE_PATH instead. First upgrade to a recent guix with + +: mkdir ~/opt +: guix pull -p ~/opt/guix-pull + +It should upgrade (ignore the locales warnings). You can optionally +specify the specific git checkout of guix with + +: guix pull -p ~/opt/guix-pull --commit=f04883d + +which is useful when you ned to roll back to an earlier version +(sometimes our channel goes out of sync). Next, we install +GeneNetwork2 with + +: source ~/opt/guix-pull/etc/profile +: git clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics +: cd ~/guix-bioinformatics +: git pull +: env GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2 + +you probably also need guix-past (the upstream channel for older packages): + +: git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past +: cd ~/guix-past +: git pull +: env GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2 + +ignore the warnings. Guix should install the software without trying +to build everything. If you system insists on building all packages, +try the `--dry-run` switch and fix the [[https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html][substitutes]]. You may add the +`--substitute-urls="http://guix.genenetwork.org https://ci.guix.gnu.org https://mirror.hydra.gnu.org"` switch. + +The guix.genenetwork.org has most of our packages pre-built(!). To use +it on your own machine the public key is + +#+begin_src scheme +(public-key + (ecc + (curve Ed25519) + (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#))) +#+end_src + +Once we have a GNU Guix profile, a running database (see below) and the file storage, +we should be ready to fire up GeneNetwork: * Running GN2 -Default settings for GN2 are listed in a file called -[[../etc/default_settings.py][default_settings.py]]. You can copy this file and pass it as a new -parameter to the genenetwork2 command, e.g. +Check out the source with git: -: genenetwork2 mysettings.py +: git clone git@github.com:genenetwork/genenetwork2.git +: cd genenetwork2 -or you can set environment variables to override individual parameters, e.g. +Run GN2 with above Guix profile -: env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2 +: export GN2_PROFILE=$HOME/opt/genenetwork2 +: env TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev the debug and logging switches can be particularly useful when -developing GN2. +developing GN2. Location and files are the current ones for Penguin2. + +It may be useful to tunnel the web server to your local browser with +an ssh tunnel: + +If you want to test a service running on the server on a certain +port (say 8202) use + + ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org + +And browse on your local machine to http://localhost:8202/ * Run gn-proxy GeneNetwork requires a separate gn-proxy server which handles -authorisation and access control. For instructions see the [[https://github.com/genenetwork/gn-proxy][README]]. +authorisation and access control. For instructions see the +[[https://github.com/genenetwork/gn-proxy][README]]. Note it may already be running on our servers! * Run Redis |