[galaxy-dev] ENA SRA data retrieval with Cloudman

2014-03-10 Thread Mohammad Heydarian
Hi Cloudman Development Team, I noticed on the most recent Cloudman release (revision 11219:5c789ab4144ahttp://bitbucket.org/galaxy/galaxy-dist/changesets/5c789ab4144a) that there is no option to Get Data from the ENA SRA. We've found that retrieving large (fastq) data sets from public databases

Re: [galaxy-dev] GATK2 (from IUC) Missing reference_genome selection

2014-03-10 Thread Björn Grüning
Hi Geert, Hi, I'm using the GATK2 tools from IUC, taken from the main toolshed. After configuration, I'm able to run the tools as standalone jobs, and everything works. When I add the job to a workflow, The 'Using reference genome' selection is empty (see screenshot in attachment for

Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies)

2014-03-10 Thread Wang, Xiaofei
Hi folks, Could anybody answer my question and help me figure it out? Thank you so much! Best, Xiaofei From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfw...@ku.edu] Sent: Thursday, March 06, 2014

[galaxy-dev] UCSC Display problem

2014-03-10 Thread Pete Schmitt
Latest version of galaxy running on CentOS 5.10 with python 2.6.8 When attempting to use display at UCSC main test There is an error at UCSC: unable to get the display-data Error from paster.log: 128.114.119.136

Re: [galaxy-dev] UCSC Display problem

2014-03-10 Thread Alper Kucukural
Hey Pete, I have exactly the same problem haven’t find a solution yet but previous versions was working without any problem. Let me know if you solve it. Alper Kucukural, PhD Bioinformatics Core, University of Massachusetts Medical School 368 Plantation St.Room AS4.2067 Worcester, MA