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| author | Pjotr Prins | 2021-08-24 10:54:01 +0200 |
|---|---|---|
| committer | Pjotr Prins | 2021-08-24 10:54:01 +0200 |
| commit | 8a8dcba497e8f4210329f42cd4b4e766d95a36fc (patch) | |
| tree | 6158b8b748b24911ccc1950ded77da067c825b9e /doc/README.org | |
| parent | ba1dd2c354863536f2c12a25b5e59aed56a683b6 (diff) | |
| download | genenetwork2-8a8dcba497e8f4210329f42cd4b4e766d95a36fc.tar.gz | |
README: on installing GN2
Diffstat (limited to 'doc/README.org')
| -rw-r--r-- | doc/README.org | 27 |
1 files changed, 25 insertions, 2 deletions
diff --git a/doc/README.org b/doc/README.org index fb1781aa..1236016e 100644 --- a/doc/README.org +++ b/doc/README.org @@ -2,6 +2,7 @@ * Table of Contents :TOC: - [[#introduction][Introduction]] + - [[#check-list][Check list]] - [[#installing-guix-packages][Installing Guix packages]] - [[#creating-a-gnu-guix-profile][Creating a GNU Guix profile]] - [[#running-gn2][Running GN2]] @@ -38,6 +39,17 @@ 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]]. +* 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 @@ -107,15 +119,26 @@ Check out the source with git: Run GN2 with above Guix profile : export GN2_PROFILE=$HOME/opt/genenetwork2 -: env TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5002 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 -gunicorn-dev +: 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. 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 |