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Galaxy: Difference between revisions
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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 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. | 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 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. Bellow we will explain some basis concept of some of configure files that need sto be setup in our HPC environment, however, we are not able to cover all concepts as they are out of this scope. | * config: It contains all require configure files to setup and optimize Galaxy. Bellow we will explain some basis concept of some of configure files that need sto be setup in our HPC environment, however, we are not able to cover all concepts as they are out of this scope. In original galaxy package this directory is located within <code>galaxy</code> directory. | ||
* galaxy: It contains the core python scripts of Galaxy. | * galaxy: It contains the core python scripts of Galaxy. | ||
* logs: Contains all log files during server Stop/Start/Run process as well as. The most important file in this directory is <code>galaxy.log</code> that is widely used to diagnose issues during Galaxy run. | * logs: Contains all log files during server Stop/Start/Run process as well as. The most important file in this directory is <code>galaxy.log</code> that is widely used to diagnose issues during Galaxy run. | ||
* plugins: Contains all plugins. In original galaxy package this directory is located in | |||
=== Galaxy configuration === | === Galaxy configuration === | ||