Re: [galaxy-dev] Invalid job runner: drmaa
Hi, I found the error. sh run.sh worked fine. So, I added some lines to my galaxy script service to load environnement variables : . /etc/profile.d/settings.sh . /etc/profile.d/drmaa.sh Now it works, but I still have some warning when I run a megablast : An error occurred running this job: *'num_threads' is currently ignored when 'subject' is specified. WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched *However I can download the result file. Best Regards, Thanks for help, Remy 2011/7/27 remy d1 remy...@gmail.com Hi Ka Ming, Thanks for your answer, but I already checked this for my galaxy user (and for root) on both the galaxy frontend node and on each node all over the cluster. It's the same path as yours for me. If you have any other idea It would be great ! :) Regards, Remy 2011/7/26 Ka Ming Nip km...@bcgsc.ca Hi, You may want to check whether your env variables are exported properly. For example, $ env DRMAA_LIBRARY_PATH=/opt/sge/lib/lx24-amd64/libdrmaa.so.1.0 Hope that helps! Ka Ming From: galaxy-dev-boun...@lists.bx.psu.edu [ galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of remy d1 [ remy...@gmail.com] Sent: July 26, 2011 7:44 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Invalid job runner: drmaa Hi, I try to configure Galaxy with SGE. It works one time yesterday but now I have the following message all the time : galaxy.jobshttp://galaxy.jobs DEBUG 2011-07-26 16:50:54,002 dispatching job 118 to drmaa runner galaxy.jobshttp://galaxy.jobs ERROR 2011-07-26 16:50:54,002 put(): (118) Invalid job runner: drmaa [ An error occurred running this job: Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. ] On the web page. Here is my universe_wsgi.ini file : [server:main] port = 8000 host = X.X.X.X use_threadpool = True [filter:proxy-prefix] prefix = /galaxy [app:main] paste.app_factory = galaxy.web.buildapp:app_factory filter-with = proxy-prefix database_connection = mysql://galaxy:xx@localhost :3306/galaxy?unix_socket=/var/run/mysqld/mysqld.sock file_path = database/files new_file_path = database/tmp job_working_directory = database/users_space/user_galaxy cluster_files_directory = database/users_space/user_galaxy use_nglims = False nglims_config_file = tool-data/nglims.yaml 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 log_events = True log_actions = True debug = True use_interactive = True library_import_dir = /home/galaxy/galaxy-dist/tmpdir user_library_import_dir = True allow_library_path_paste = True admin_users = me@... enable_pages = True enable_api = True set_metadata_externally = True retry_metadata_internally = True outputs_to_working_directory = True start_job_runners = drmaa default_cluster_job_runner = drmaa:/// [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:/// [galaxy_amqp] I checked many things, but it did not change anything... Any help would gracefull. Regards. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Invalid job runner: drmaa
On Thu, Jul 28, 2011 at 10:49 AM, remy d1 remy...@gmail.com wrote: Hi, ... Now it works, but I still have some warning when I run a megablast : An error occurred running this job: 'num_threads' is currently ignored when 'subject' is specified. You get that warning message from the current BLAST+ binaries - you can ignore it. (The previous release of BLAST+ sometimes crashed in this mode, so in the current release 2.2.25+ the NCBI just made it single threaded, and I hope the next release will actually fix it). Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Invalid job runner: drmaa
Hi Ka Ming, Thanks for your answer, but I already checked this for my galaxy user (and for root) on both the galaxy frontend node and on each node all over the cluster. It's the same path as yours for me. If you have any other idea It would be great ! :) Regards, Remy 2011/7/26 Ka Ming Nip km...@bcgsc.ca Hi, You may want to check whether your env variables are exported properly. For example, $ env DRMAA_LIBRARY_PATH=/opt/sge/lib/lx24-amd64/libdrmaa.so.1.0 Hope that helps! Ka Ming From: galaxy-dev-boun...@lists.bx.psu.edu [ galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of remy d1 [ remy...@gmail.com] Sent: July 26, 2011 7:44 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Invalid job runner: drmaa Hi, I try to configure Galaxy with SGE. It works one time yesterday but now I have the following message all the time : galaxy.jobshttp://galaxy.jobs DEBUG 2011-07-26 16:50:54,002 dispatching job 118 to drmaa runner galaxy.jobshttp://galaxy.jobs ERROR 2011-07-26 16:50:54,002 put(): (118) Invalid job runner: drmaa [ An error occurred running this job: Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. ] On the web page. Here is my universe_wsgi.ini file : [server:main] port = 8000 host = X.X.X.X use_threadpool = True [filter:proxy-prefix] prefix = /galaxy [app:main] paste.app_factory = galaxy.web.buildapp:app_factory filter-with = proxy-prefix database_connection = mysql://galaxy:xx@localhost :3306/galaxy?unix_socket=/var/run/mysqld/mysqld.sock file_path = database/files new_file_path = database/tmp job_working_directory = database/users_space/user_galaxy cluster_files_directory = database/users_space/user_galaxy use_nglims = False nglims_config_file = tool-data/nglims.yaml 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 log_events = True log_actions = True debug = True use_interactive = True library_import_dir = /home/galaxy/galaxy-dist/tmpdir user_library_import_dir = True allow_library_path_paste = True admin_users = me@... enable_pages = True enable_api = True set_metadata_externally = True retry_metadata_internally = True outputs_to_working_directory = True start_job_runners = drmaa default_cluster_job_runner = drmaa:/// [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:/// [galaxy_amqp] I checked many things, but it did not change anything... Any help would gracefull. Regards. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Invalid job runner: drmaa
Hi, I try to configure Galaxy with SGE. It works one time yesterday but now I have the following message all the time : galaxy.jobs DEBUG 2011-07-26 16:50:54,002 dispatching job 118 to drmaa runner galaxy.jobs ERROR 2011-07-26 16:50:54,002 put(): (118) Invalid job runner: drmaa [ An error occurred running this job: *Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.* ] On the web page.* * Here is my universe_wsgi.ini file : [server:main] port = 8000 host = X.X.X.X use_threadpool = True [filter:proxy-prefix] prefix = /galaxy [app:main] paste.app_factory = galaxy.web.buildapp:app_factory filter-with = proxy-prefix database_connection = mysql://galaxy:xx@localhost :3306/galaxy?unix_socket=/var/run/mysqld/mysqld.sock file_path = database/files new_file_path = database/tmp job_working_directory = database/users_space/user_galaxy cluster_files_directory = database/users_space/user_galaxy use_nglims = False nglims_config_file = tool-data/nglims.yaml 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 log_events = True log_actions = True debug = True use_interactive = True library_import_dir = /home/galaxy/galaxy-dist/tmpdir user_library_import_dir = True allow_library_path_paste = True admin_users = me@... enable_pages = True enable_api = True set_metadata_externally = True retry_metadata_internally = True outputs_to_working_directory = True start_job_runners = drmaa default_cluster_job_runner = drmaa:/// [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:/// [galaxy_amqp] I checked many things, but it did not change anything... Any help would gracefull. Regards. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
