[galaxy-dev] uploading multi-file archives and creation of potentially large collections

2016-08-04 Thread Stephan Oepen
colleagues, in our adaptation of galaxy for large-scale natural language processing, a fairly common use pattern is to invoke a workflow on a potentially large number of text files. hence, i am wondering about facilities for uploading an archive (in ‘.zip’ or ‘.tgz’ format, say) containing severa

Re: [galaxy-dev] Removing job in error state

2016-08-04 Thread Ryan G
Thanks. That fixed it. On Thu, Aug 4, 2016 at 3:19 AM, Hans-Rudolf Hotz wrote: > Hi Ryan > > If the "Stop Jobs" option on the Admin page does not work, you can go for > the direct way by manually interacting with the PostgreSQL database: > > Change the state to "error" in the 'job' table, eg:

[galaxy-dev] Retrieving bam index file for visualization outside of Galaxy

2016-08-04 Thread Ouellette, Scott
Hi all, I have a use case where I need to programmatically download both the .bam and it's index file to run IGV outside of Galaxy, but have not found a straightforward way to do so. It seems that Galaxy always generates this .bai file under the hood, and I can download it manually by clicking

Re: [galaxy-dev] Removing job in error state

2016-08-04 Thread Hans-Rudolf Hotz
Hi Ryan If the "Stop Jobs" option on the Admin page does not work, you can go for the direct way by manually interacting with the PostgreSQL database: Change the state to "error" in the 'job' table, eg: update job set state='error' where id=12772; As always, be very careful when you direct