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: email@example.com >> 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.jobs<http://galaxy.jobs> DEBUG 2011-07-26 16:50:54,002 dispatching >> job 118 to drmaa runner >> galaxy.jobs<http://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:xxxxxx@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. >> > >
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