[galaxy-dev] Error preparing job

2011-07-25 Thread SHAUN WEBB
Hi all, I'm getting the following error running a custom tool. I'm not really sure where the problem is coming from, it doesn't happen every time I run the tool. Can anyone point me in the right direction? Thanks Shaun Traceback (most recent call last): File

Re: [galaxy-dev] Error preparing job - PLEASE IGNORE PREVIOUS

2011-07-25 Thread SHAUN WEBB
Ignore previous email, I found the error, it was not a Galaxy problem Thanks Shaun Quoting SHAUN WEBB swe...@staffmail.ed.ac.uk on Mon, 25 Jul 2011 11:21:43 +0100: Hi all, I'm getting the following error running a custom tool. I'm not really sure where the problem is coming from, it

Re: [galaxy-dev] Saved Histories - default view on deleted histories (bug)

2011-07-25 Thread Yuelin Zhu
Hi Jeremy, I updated my local Galaxy and see items in the Saved Histories display normally. Thank you so much for the fix. Excellent work. Jack On 21 July 2011 10:07, Jeremy Goecks jeremy.goe...@emory.edu wrote: Jack, Thanks for following up on this issue. I've fixed the problem in

Re: [galaxy-dev] Question about dependency management

2011-07-25 Thread Jennifer Jackson
Hello Indresh, Apologies for the delay in reply, please see below: On 7/13/11 1:55 PM, Singh, Indresh wrote: Greetings, We installed Galaxy at JCVI for internal user but we are discovering that we are missing lots of third party tools/dependencies. My question; is there any script/tool that

Re: [galaxy-dev] Upload of images - jpg/png - binary file contains inappropriate content

2011-07-25 Thread Jelle Scholtalbers
Hi Greg, this was indeed causing the problem. I added some code which now allows to sniff image files. It is practically untested (it does work for me on bmp, jpg, png, tiff) - didn't try with PIL although the code is there. Attached are diffs against changeset 058a5d7a4f84 (bit outdated - can

[galaxy-dev] set_matadata_externally =True

2011-07-25 Thread Chorny, Ilya
I am still working on the patch to submit jobs as the actual user under SGE . I have it working for the default case but it fails for the case of set_metadata_externally = TRUE. Can someone point me to where the metadata files are created so that I can change the permissions for those files?