galaxy-project-management

PART 1 - patching and copying

clone the repo to your /tmp directory and run

./deploy.sh run-type

run-type can "dry-run" or "real". Null value defaults to "dry-run".

The script will place all the neccessary files for project management and resource allocation.

PART 2 - configuration

To enable the changes in the menu (Project Admin Tab):

cd GALAXY_ROOT
make client

Create a file (only if you don't 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

Add a line into galaxy.ini file containing the emails of all Project Administrators (GOLD adminstrators)

project_admin_users = <EMAIL LIST>  

This seems to be fixed in 16.10, please check!!

The code displaying the job parameters contains a list of projects accessible to a user. To enable this feature, the file:

GALAXY_ROOT/config/job_resource_params_conf.xml

shall contain a parameter with name = "project" and the option "gx_default", e.g.

	<param label="Project" name="project" type="text" value="" help="Project to assign resource allocation to. Leave blank to use default value.">
            <option value="gx_default">Lifeportal default project</option>
    </param>

Edit /etc/sudoers :

add the following lines

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

and edit the hostname to match your hostname's name

Edit the file /home/galaxy/galaxy/.venv/bin/activate :

add the following lines to the bottom of file

export GALAXY_LIB=/home/galaxy/galaxy/lib  
export PYTHONPATH=$GALAXY_LIB:/home/galaxy/galaxy/lib/usit/python  
echo "PYTHONPATH SET IN .venv/bin/activate " $PYTHONPATH  

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