Re: [galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster

2011-11-04 Thread Carlos Borroto
Hi Jen, Thanks for the quick response. The workaround you describe could work, but I might run into trouble later on. My interest is to develop a workflow for GATK, which have very strict requirements on the input BAM file. One of which is that the sorting have to be exactly the same as the

[galaxy-dev] Error when clicking on published workflows

2011-11-04 Thread Chorny, Ilya
URL: http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test Module paste.exceptions.errormiddleware:143 in __call__ http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-04 Thread Chorny, Ilya
I am getting a strange error when I am uploading a file mv: inter-device move failed: `/illumina/scratch/Swim/galaxy/tmpk2sbZl' to `/home/galaxy/ichorny/galaxy-central/database/tmp/upload_file_data_isAnwO'; unable to remove target: Permission denied I figured out that the mv is coming from

Re: [galaxy-dev] Looks like actual user breaks splitting

2011-11-04 Thread Chorny, Ilya
Looks like the mv is something I added and forgot about. I changed it to shutil.copyfile and it works fine. This also has something to do with the isilon. I pushed it to the actual user repository so you can check it out. Have a good weekend. Thanks, Ilya -Original Message- From:

Re: [galaxy-dev] Ucsc bigbed display tool does not show up on local installation

2011-11-04 Thread Jeremy Villalobos
Thanks for your response. I figured out it was some extra text at the end of the xml file that was preventing galaxy from reading the file. I also was confused about how to setup the proxy. For Ubuntu, the apache2 configuration file is in /etc/apache2/sites-available/default (using virtual