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Hi all,
We are using an instance of galaxy workflow management system (http://galaxy.psu.edu/) that will launch jobs on our local SGE based cluster. The initial setup went smooth and the Galaxy seemed to be working fine with the cluster and MySQL database.
The issue we are facing is that sometimes in a workflow, a second step queued job starts without waiting for finishing the first step. I assume it is related to our galaxy config file and we might misconfigured it somewhere.
Below is our galaxy config file (univers_wsgi.ini).
If someone here has experience with this tool, any help would be greatly appreciated.
We are using an instance of galaxy workflow management system (http://galaxy.psu.edu/) that will launch jobs on our local SGE based cluster. The initial setup went smooth and the Galaxy seemed to be working fine with the cluster and MySQL database.
The issue we are facing is that sometimes in a workflow, a second step queued job starts without waiting for finishing the first step. I assume it is related to our galaxy config file and we might misconfigured it somewhere.
Below is our galaxy config file (univers_wsgi.ini).
If someone here has experience with this tool, any help would be greatly appreciated.
Code:
[server:main] use = egg:Paste host = 0.0.0.0 use_threadpool = True threadpool_workers = 10 [filter:gzip] use = egg:Paste#gzip [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] paste.app_factory = galaxy.web.buildapp:app_factory database_connection = mysql://galaxy:galaxy@localhost/galaxydb1?unix_socket=/var/lib/mysql/mysql.sock database_engine_option_pool_recycle = 7200 file_path = database/files new_file_path = database/tmp smtp_server = /usr/sbin/sendmail mailing_join_addr = error_email_to = brand = NGS static_enabled = True static_cache_time = 360 static_dir = %(here)s/static/ static_images_dir = %(here)s/static/images static_favicon_dir = %(here)s/static/favicon.ico static_scripts_dir = %(here)s/static/scripts/ static_style_dir = %(here)s/static/june_2007_style/blue debug = False use_interactive = False library_import_dir = database/upload_directory user_library_import_dir = database/user_library_import allow_library_path_paste = true admin_users = require_login = True allow_user_creation = False allow_user_deletion = True enable_pages = True track_jobs_in_database = True enable_job_recovery = True set_metadata_externally = True retry_metadata_internally = False local_job_queue_workers = 5 start_job_runners = drmaa default_cluster_job_runner = drmaa:/// cluster_job_queue_workers = 1 [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = local:/// ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:///
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