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.d1@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 <kmnip@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-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of remy d1 [remy.d1@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.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.