Galaxy: Difference between revisions

All files in <code>config</code> directory are used to configure your Galaxy server. Configuring and optimizing Galaxy is very tricky and requires a broad scientific and technical knowledge and explaining all of them is beyond our topic. We assume users who are requiring galaxy have knowledge to further setup its own galaxy instance. Here we explain some important and basic setup that needed to be done by admin in order to server to work. We recommend to go though configure files and set them up appropriately. However, we strongly recommend not to overwrite the following variables that are set by the admin. Here are some of those variables:

* File <code>galaxy.yml</code>: its most important and the main configure  file. The following variables are set in this file:

** <code>http:</code> contain your unique port number

** <code>database_connection</code> the name of your Galaxy database and your database server.

** <code>virtualenv</code> the path to python virtual environment in gateway machine

** <code>file_path, new_file_path, tool_config_file, shed_tool_config_file, tool_dependency_dir, tool_data_path, visualization_plugins_directory, job_working_directory, cluster_files_directory, template_cache_path, citation_cache_data_dir, citation_cache_lock_dir</code> setup appropriate paths for tools, tool sheds and dependencies.

* <code>job_conf.xml</code>: All variables in this files is used in job submission to cedar. Various packages have different job specification, for example package "spades" uses 8 cores with the walltime of 3 hours and job will be submission under your default group name <code>def-xxxxx</code>. Please take a look at this file and setup your desire job specification. Note that any change in these configuration files requites to restart  the server.