Hi Stephan, I am no expert with PBS but your default_job_runner looks wrong Instead of default_cluster_job_runner = drmaa://uv100.awi.de/slong/ you should use some PBS specific paramters for the drmaa:/// part. I am using SGE an specifiy some of the qsub parameters: default_cluster_job_runner = drmaa://-pe make 16 -q bioinf.q/ this submits the job to our bioinf-cluster on a node with 16 free slots. So you should check how you submit jobs via commandline with PBS and use these paramaters for setting drmaa:/// Cheers, Sascha Kastens Project Manager   GATC Biotech AG Jakob-Stadler-Platz 7 D-78467 Konstanz   Phone: +49 (0) 7531-81604110 Fax:     +49 (0) 7531-816081 Email:  s.kastens@gatc-biotech.com   http://www.gatc-biotech.com http://www.twitter.com/gatcbiotech http://www.facebook.com/gatcbiotech http://www.xing.com/companies/gatcbiotechag   GATC Biotech AG Chairman Supervisory Board: Fritz Pohl Board of Directors: Peter Pohl, Thomas Pohl, Dr. Marcus Benz UID: DE 142 315 733 | Registration: Konstanz, HRB 1757 | Registered Office: Konstanz     The information contained in this email is intended solely for the addressee. Access to this email by anyone else unauthorized. If you are not the intended recipient, any form of disclosure, reproduction, distribution or any action taken or refrained from in reliance on it, is prohibited and may be unlawful. Please notify the sender immediately. The content of this email is not legally binding unless confirmed by letter.   Original Message processed by CONSOLIDATE Subject: [galaxy-dev] PBSpro Cluster Server possible? Sent: Dienstag, 24. Juli 2012 12:23 From: Stephan Frickenhaus (Stephan.Frickenhaus@awi.de) Hello, I have tried to couple our GALAXY-server (unified, running on a virtual server, ubuntu 12) with our big SGI Cluster-Server uv100 running PBSpro as job system (pbs_version = PBSPro_11.1.1.112253). On the GALAXY-server I have installed ii  pbs-drmaa-dev                        1.0.10-2                       DRMAA for Torque/PBS Pro - devel ii  pbs-drmaa1                           1.0.10-2                       DRMAA for Torque/PBS Pro - runtime We have the GALAXY-sources installed very recently; job-creation is prepared, but no job is scheduled to our uv100. Did you ever hear that the libdrmaa.so coming with this package is useful to couple to a PBSpro-server? The DRMAA_LIBRARY_PATH  has been set accordingly to  /usr/lib/libdrmaa.so.1.0.10 . we set default_cluster_job_runner = drmaa://uv100.awi.de/slong/ We also checked that the torque-system on the GALAXY-Server could successfully submit jobs by "qsub" on the PBSpro-server in the slong queue. Best regards and many thanks in advance,   S. Frickenhaus -- -- Prof. Dr. Stephan Frickenhaus Hochschule Bremerhaven An der Karlstadt 8 27568 Bremerhaven 0471-4823-525 0151-1741 1631   Alfred-Wegener-Institut f. Polar- u. Meeresforschung Am Handelshafen 12 27570 Bremerhaven stephan.frickenhaus@awi.de 0471-4831-1179  0151-1741 1631       -- Prof. Dr. Stephan Frickenhaus FB1 - Biotechnologie  Hochschule Bremerhaven An der Karlstadt 8 27568 Bremerhaven 0471-4823-525 0151-1741 1631   Alfred-Wegener-Institut f. Polar- u. Meeresforschung Bioinformatik/Rechenzentrum Am Handelshafen 12 27570 Bremerhaven stephan.frickenhaus@awi.de 0471-4831-1179 0151-1741 1631