[galaxy-dev] Unable to run jobs in Galaxy: runners/local.py # stdout_file.close() # python2.7/tempfile.py # self.unlink(self.name) # OSError: [Errno 2] No such file or directory

2012-11-20 Thread Tim te Beek
Hi all Since updating to the latest Galaxy-dist version, I'm unable to run any jobs. galaxy.jobs.handler INFO 2012-11-20 12:22:09,018 (6403) Job dispatched galaxy.objectstore CRITICAL 2012-11-20 12:22:15,362 /home/galaxy/galaxy-dist/database/job_working_directory/006/6403 delete error [Errno 2] N

[galaxy-dev] param.dynamic_options: How can I disable escaping HTML tags?

2012-05-22 Thread Tim te Beek
Hi all, Up until today I was happily using the following to produce the options for a Galaxy tool of mine based on a daily updated remote resource: """ ... """ The get_complete_genomes() call returns and iterator with tuples of ("Label", "Value", False), which are shown to the user. Previously

Re: [galaxy-dev] How to allow anonymous users to run workflows?

2012-01-29 Thread Tim te Beek
e happy using this approach. Best, Tim On Tue, Sep 6, 2011 at 5:00 PM, Tim te Beek wrote: > I completely agree it's a bit of an unfortunate requirement in this > case, but I'm not averse to (minor) code changes to achieve a more > polished user experience. Something like the be

[galaxy-dev] Galaxy tools with redirected python logging output get stuck past a certain amount of logging output

2011-10-06 Thread Tim te Beek
Hi all, I've got some Python applications that I've hooked into Galaxy, which use the Python logging module for output. To capture this output in my Galaxy history I've created a wrapper that adds a logging.FileHandler to the root logger, which uses an Galaxy tool output argument as file to write

Re: [galaxy-dev] How to allow anonymous users to run workflows?

2011-09-06 Thread Tim te Beek
ccount with a throw away email address - it's only for password > recovery. > Clearly registration is not mandatory - just sensible and free, so the > journal's off your back. Hope that demo account isn't multitasking too > often. > > On Tue, Sep 6, 2011 at 6:17 PM

[galaxy-dev] How to allow anonymous users to run workflows?

2011-09-06 Thread Tim te Beek
Hi all, Was wondering how I can allow anonymous users to run workflows in my local Galaxy instance, as currently users need to be logged in to run workflows. I'd like drop this requirement in light of the intended publication of a workflow in a journal which demands that "Web services must not req