[galaxy-dev] Bug in history when using Admin account ??

2013-05-17 Thread Neil.Burdett
Hi, I believe I have found a bug? Or maybe I'm not using Galaxy correctly? These are the steps I used: * Downloaded the latest version of Galaxy * Created a user m...@me.commailto:m...@me.com * Uploaded several files * Logged out * Create a user

Re: [galaxy-dev] Bug in history when using Admin account ??

2013-05-17 Thread Hans-Rudolf Hotz
Hi Neil Just double checking: Have you looked at the list of 'Saved Histories'? For each user, you probably have several histories called 'Unnamed history' and one of them may contain the data you uploaded previously. Whenever you log out and log in as a different user, a new, empty history

Re: [galaxy-dev] Bug in history when using Admin account ??

2013-05-17 Thread Neil.Burdett
Hans, You are correct. When I look at the Save Histories and I double click on them I can see everything. Thanks for the help Neil -Original Message- From: Hans-Rudolf Hotz [mailto:h...@fmi.ch] Sent: Friday, 17 May 2013 4:58 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc:

Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

2013-05-17 Thread Joachim Jacob | VIB |
Allright. I just pulled in all changesets from stable to my cloud Galaxy, restarted, and everything works, at first glance. Thanks for your support! J Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be

[galaxy-dev] Workflow: multiple input errors

2013-05-17 Thread Joachim Jacob | VIB |
Hi all, I have fired up an cloud instance of Galaxy, 2 persistent nodes, scalable up to 10. I have updated the code to the latest stable, after issues with not being able to select multiple input for workflows (more background:

Re: [galaxy-dev] Handling of tool_dependencies.xml errors in Tool Shed testing

2013-05-17 Thread Peter Cock
Hi again, I've realised that my current Blast2GO install script would be a perfect example of where this tweak to fabric_util.py would help - when I wrote the tool_dependencies.xml I didn't appreciate that the download_by_url action was only allowed as the first action - currently it is ignored

[galaxy-dev] Test Tool Shed uploads broken

2013-05-17 Thread Peter Cock
Hi Greg Dave, I just tried to upload an update to my Blast2GO wrapper on the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go This gave the following error, also note typo sucessfully [sic] - successfully. Internal Server Error Galaxy was unable to sucessfully complete

Re: [galaxy-dev] Test Tool Shed uploads broken

2013-05-17 Thread Greg Von Kuster
Hi Peter, Thanks for letting me know and sorry about the inconvenience. I've fixed this in 9763:9c06caa86e2a which is now on the test tool shed. Greg Von Kuster On May 17, 2013, at 5:08 AM, Peter Cock wrote: Hi Greg Dave, I just tried to upload an update to my Blast2GO wrapper on the

Re: [galaxy-dev] Workflow: multiple input errors

2013-05-17 Thread Joachim Jacob | VIB |
It is most likely due to the cluster configuration, since on our non-cluster production machine doesn't have this behaviour. Cheers, J Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 05/17/2013 10:16 AM, Joachim Jacob | VIB | wrote: Hi all, I have fired up

[galaxy-dev] Add a download process to a job handler in history queue

2013-05-17 Thread Zinonas Antoniou
Hello, I developed a script to download file to Galaxy from other platform. If the size of the file is large, the process may take several minutes and I can't to anything else in Galaxy. Is there a way to add the download process in a job handler and add it to history queue? Any help is

Re: [galaxy-dev] Test Tool Shed uploads broken

2013-05-17 Thread Peter Cock
On Fri, May 17, 2013 at 12:37 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, Thanks for letting me know and sorry about the inconvenience. I've fixed this in 9763:9c06caa86e2a which is now on the test tool shed. Greg Von Kuster Great - that works for me now :) Peter

[galaxy-dev] Cross Tool Shed dependencies / blast_datatypes

2013-05-17 Thread Peter Cock
Hi Greg, Do you guys have a rough plan for when inter-ToolShed dependencies will be supported? I've been using the Test Tool Shed to validate tools before uploading them to the main Tool Shed - this uncovers things like omitted test files which I don't find locally since I'm testing in-situ.

[galaxy-dev] Galaxy group at Google+

2013-05-17 Thread Samuel Lampa
Hi, I realized there was no Galaxy group on G+, although I find G+ is a really nice medium for some kind of posts, especially for things like showing off some work you have done, without disturbing others on the mailing lists. Feel free to chime in: http://gplus.to/galaxyportal Cheers, //

Re: [galaxy-dev] tool_dependencies inside tool_dependencies

2013-05-17 Thread John Chilton
Hey All, There was a long conversation about this topic in IRC yesterday (among people who don't actually use the tool shed all that frequently), I have posted it to the new unofficial Galaxy Google+ group if anyone would like to read and chime in.

[galaxy-dev] very long load times for some shared libraries...

2013-05-17 Thread Langhorst, Brad
All of a sudden, some larger libraries are taking a very long time to open. [cid:BB83AE73-EAE2-44B9-B294-918CDE8C18F4@neb.com] This one timed out… Anybody else seen this? Could this be a database issue? Didn't see any really long queries in the postgres log (and i log anything longer than