[galaxy-dev] Issue with job_name, UnicodeDecodeError in drmaa
Hello, I updated to the latest version (17.05) galaxy code. I was updating from a very old version. I fixed all the issues with except one. I am getting the following error when I submit a job. galaxy.jobs.runners ERROR 2017-05-29 01:42:44,008 (15131) Unhandled exception calling queue_job Traceback (most recent call last): File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 104, in run_next method(arg) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 132, in queue_job job_name = self._job_name(job_wrapper) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 397, in _job_name job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 397, in job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) else '_' for x in job_name ) UnicodeDecodeError: 'ascii' codec can't decode byte 0xa6 in position 52: ordinal not in range(128) I spent a day trying to debug this and didn’t get anywhere. The job_name looks OK. I would really appreciate some help from the community. Thanks! -Raj ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] bwa_mem and "-t" option
Hi David, this is possible via the GALAXY_SLOTS mechanism. An admin can give every tool it's own environment and can set GALAXY_SLOTS dynamically. A user can not do this, as this is highly dependent on the node this tool will run and normally a user does not know about this. However, if you really want to offer this to a user, Galaxy also offers to enable this option per tool level and will add additional parameter fields to set GALAXY_SLOTS as a user. Cheers, Bjoern Am 26.05.2017 um 20:23 schrieb David Kovalic: > Hi, > > Is it possible, and if so how, to run the galaxy devteam > (version 546ada4a9f43) of bwa_mem with the "-t" option and a value >1? > > "-t INT number of threads [1]" > > > This would be quite useful, and used, for accelerating single bwa mem jobs. > > Thanks, > > David > > > > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
