[galaxy-dev] tools fails only in workflow

2014-02-04 Thread Christian Hundsrucker
Dear all, I developed a tool which allows an optional selection as input amongst others. It works quite neat if I run it via "Analyse Data". Actually, it only breaks in one condition: If I try to run it "as a Workflow" and set the "multiple selection input" to be set at runtime AND do not sele

Re: [galaxy-dev] error with unicode output

2013-12-06 Thread Christian Hundsrucker
Is it MySQL as well? David - do you have a test setup you can hack on? I wonder if this would go away if you converted your tables to UTF-8. http://stackoverflow.com/questions/6115612/how-to-convert-an-entire-mysql-database-characterset-and-collation-to-utf-8 That is not my official recommendat

Re: [galaxy-dev] error with unicode output

2013-12-05 Thread Christian Hundsrucker
Hi David, hi all! I have a similar/the same issue in another setting... galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) [...] galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/pers

[galaxy-dev] provide group(s) association as a tool parameter

2013-07-16 Thread Christian Hundsrucker
Hi there! Is there an easy way to pass a users group associations to a tool as a parameter. Maybe similar to pass user information via the reserved variable "$__user_email__" ?! I tried "$__app__.model.UserGroupAssociation.group" however I end up with a mapper-object and are kind of stuck her

Re: [galaxy-dev] location of .loc-files/data tables -- bug or feature?

2013-05-22 Thread Christian Hundsrucker
pdate right away, we'll have another full-fledged dist release out soon. -Dannon On Tue, May 21, 2013 at 5:48 AM, Christian Hundsrucker mailto:christian.hundsruc...@ur.de>> wrote: Hello, Galaxy developers! I do a bit of tweaking to a local galaxy instance. Thus, I just

[galaxy-dev] location of .loc-files/data tables -- bug or feature?

2013-05-21 Thread Christian Hundsrucker
Hello, Galaxy developers! I do a bit of tweaking to a local galaxy instance. Thus, I just realized that subdirectories are not supported for the location of .loc-files/data tables. E.g. tool-data/somesub/my.loc is not recognized even if this location is correctly linked in the tool_data_table_c

[galaxy-dev] How to retain files compressed

2011-02-28 Thread Christian Hundsrucker
lse try: header = open( filename ).read(4) #(4)=>4Bytes if binascii.b2a_hex( header ) == binascii.hexlify( 'RDX2' ): #check if there is the RDX2 signature return True return False