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 + "glyx". For example if PI username is "davidc" the galaxy top directory will "daglxy" and it is located in <code>/project/group name/</code> were <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 require configure files to setup and optimize Galaxy server. Bellow we will explain some basis concepts of some of configure files that need to be setup in order to be compatible with our HPC environment, however, we are not able to cover all concepts as they beyond of this topic.   

* 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 would be written in <code>server.log</code> while all messages during the run would be written in <code>galaxy.log</code>.   

* plugins: Contains all plugins. In original galaxy package this directory is located within <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 dependency packages that is needed for tool sheds. By default packages in this directory are being installed using anaconda.  

* database: It contains input/output and error files of all job that run in cluster nodes.