Galaxy: Difference between revisions

Galaxy is usually installed on the project directory of the group and it contains several sub-directories. The name of the Galaxy top directory is determined by taking the first two character of PI username + "glxy". For example if PI username is "davidc" the Galaxy top directory will "daglxy" and it is located in <code>/project/group name/</code> where <code>group name</code> is the default group name of PI, eg., <code>def-davidc</code>. Galaxy main directory contains the following sub-directories which is slightly different than the original Galaxy package.

* config: It contains all required configuration files to set up and optimize the Galaxy server. Below we explain some basic concepts of some of configuration files that need to be set up in order to be compatible with our HPC environment, however, we will not cover all concepts.   

* galaxy: It contains the core Galaxy package which is written mostly in Python.  

* logs: Contains two files, <code>galaxy.log</code> and <code>server.log</code>.  All messages during startup or shutdown of the server are written in <code>server.log</code> while all messages during the run are written in <code>galaxy.log</code>.   

* plugins: Contains all plugins. In original Galaxy package this directory is located in the <code>galaxy</code> directory.  

* tmp: Contains all temporary files that Galaxy needs for compiling and installing tool sheds.  

* venv: It is a Python virtual environment directory and it contains all Python package dependencies.

* tool-data: It contains data used by tools. See the samples in [https://galaxyproject.org/admin/data-integration data-integration]

* tool-dependencies: It contains all packages needed for tool sheds. By default packages in this directory are installed using Anaconda.  

* database: It contains input, output, and error files of all jobs that run on cluster nodes.