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galaxy-core-management

Prerequistes

  • If using data from existing galaxy and gold databases, these should be dumped and imported to the current databases

The script deploys:

  • Galaxy framework
  • SLURM rpms
  • Munge rpms
  • Polish DRMAA library
  • Project management module
  • Customized drmaa solution

Configures

  • Galaxy main config file (galaxy.ini)
  • Galaxy job_resource_params.xml (job parameters file for the cluster)
  • Galaxy custom environment file (local_env.sh)
  • file (.venv/bin/activate) which sets the path for the custom python packs (like drmaa_usit.py)

Deploying

clone the repo to your /tmp directory and run

./deploy_full_procedure.sh

Follow the procedures in the script. The script will deploy the setup of the features mentioned above. Please refer to the final requirements which will be displayed at the end of the script execution.

Create a file (only if you DO NOT take the file over from a previous version)

/work/projects/galaxy/external_dbs/project_managers.txt

which shall contain all the project managers. This file is called by the controller lib/usit/python/Project_managers.py

Edit /etc/sudoers :

This file should be edited with visudo, to avoid syntax errors. Visudo uses the editor set by the EDITOR environment variable. You can use nano this way:

sudo EDITOR=nano visudo

add the following lines

Cmnd_Alias GOLD = /opt/gold/bin/*
Defaults:galaxy !requiretty
galaxy <HOSTNAME>=(gold) NOPASSWD: GOLD

where is the hostname of the server.

ATTENTION : In order to use the project management feature, GOLD shall be running on your Galaxy instance!

Issues

  • /etc/init.d/galaxyd is not modified according to settings.sh, and may need manual changes.

Filesender files :

There have been added blocks into

setting-template.sh
local_env.sh

Scripts (called by deploy_full_procedure.sh):

deploy_filesender_apache_config.sh
deploy_filesender_code.sh
deploy_filesender_galaxy_config.sh
deploy_filesender_simplesamlphp_code.sh

Configuration files

filesender.conf
filesender-php.ini
php.conf
config-filesender.php
saml20-idp-remote.php

Customized files (to be copied)

site_splash.html.php