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Galaxy: Difference between revisions
→Galaxy configuration
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All files in directory <code>config</code> are used to configure your Galaxy instance. Configuring and optimizing Galaxy is very tricky and requires a broad scientific and technical knowledge and explaining all of them is by far out this scope. We assume users who are requiring galaxy have enough knowledge to further setup its own galaxy instance. Here we explain the most important and basic setup that has been done by admin in order Galaxy to just work. We strongly recommend not to overwrite thesed variable. Here are some of those setup: | All files in directory <code>config</code> are used to configure your Galaxy instance. Configuring and optimizing Galaxy is very tricky and requires a broad scientific and technical knowledge and explaining all of them is by far out this scope. We assume users who are requiring galaxy have enough knowledge to further setup its own galaxy instance. Here we explain the most important and basic setup that has been done by admin in order Galaxy to just work. We strongly recommend not to overwrite thesed variable. Here are some of those setup: | ||
* File galaxy.yml: its most important and the main configure file. We setup the following variables: | * File <code>galaxy.yml</code>: its most important and the main configure file. We setup the following variables: | ||
** <code>http:</code> contain your unique port number | ** <code>http:</code> contain your unique port number | ||
** <code>database_connection</code> the name of your Galaxy database and your database server. | ** <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>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>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 is submission under your default group name <code>def-xxxxx</code>. Please take a look at this file and setup your desire job specification. | |||