Re: [galaxy-dev] GalaxyToolShed: 'Contact owner'

2012-01-13 Thread Greg Von Kuster
Hi Marcel, Requiring users to be logged in in order to contact the owner of a repository significantly hinders spam emails. On Jan 12, 2012, at 9:04 PM, Marcel Schumann wrote: Hi Greg, sure, that's right. But I checked it for my own repository _without_ being logged in ... and for other

Re: [galaxy-dev] Picard MarkDups

2012-01-13 Thread Nate Coraor
On Jan 12, 2012, at 11:37 AM, Ryan Golhar wrote: I'm trying to run Picard MarkDups through Galaxy. Picard is using the standard 4g for the java max heap size. I need to increase this. Is it possible to offer this as an option to the user? If not, where do I change this? I see the entry

Re: [galaxy-dev] Status on importing BAM file into Library does not update

2012-01-13 Thread Nate Coraor
On Jan 12, 2012, at 11:41 PM, Ryan Golhar wrote: Any ideas as to how to fix this? We are interested in using Galaxy to host all our NGS data. If indexing on the head node is going to happen, then this is going to be an extremely slow process. Could you post the contents of

Re: [galaxy-dev] Galaxy Hang after DrmCommunicationException

2012-01-13 Thread Ann Black
Thanks so much! I have applied the fix to our env. In looking over the logic, there was an existing exception block that would have caught the communication exception generically ­ but the job moved (in this scenario erroneously) the job into a failure workflow. I would like to understand what

Re: [galaxy-dev] Fwd: tool restrict access

2012-01-13 Thread Ivan Merelli
Hi Jeremy, sorry for bother you again. I do some tests and the problem seems not in the semi-colons (the cheetah manual is not very clear in this sense, I put them but it did not solve the problem), but in the display tag which is simply incorrect in that position, a call to a python script is

Re: [galaxy-dev] Status on importing BAM file into Library does not update

2012-01-13 Thread Ryan Golhar
I re-uploaded 3 BAM files using the Upload system filepaths On Fri, Jan 13, 2012 at 10:53 AM, Nate Coraor n...@bx.psu.edu wrote: On Jan 12, 2012, at 11:41 PM, Ryan Golhar wrote: Any ideas as to how to fix this? We are interested in using Galaxy to host all our NGS data. If indexing on the

Re: [galaxy-dev] Status on importing BAM file into Library does not update

2012-01-13 Thread Ryan Golhar
I re-uploaded 3 BAM files using the Upload system file paths. runner0.log shows: galaxy.jobs DEBUG 2012-01-13 12:50:08,442 dispatching job 76 to pbs runner galaxy.jobs INFO 2012-01-13 12:50:08,555 job 76 dispatched galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:08,697 (76) submitting file

Re: [galaxy-dev] Fwd: tool restrict access

2012-01-13 Thread Jeremy Goecks
May you suggest me how to sketch a simple python script that prints in the central section of the galaxy window a message like you are not authorized to execute this tool ? This isn't possible right now, hence my reference to the open Bitbucket issue regarding this limitation. The best you

Re: [galaxy-dev] Galaxy Hang after DrmCommunicationException

2012-01-13 Thread Edward Kirton
i had seen the job process die with this error: if state != old_state: UnboundLocalError: local variable 'state' referenced before assignment since the DRM timeout is an intermittent error, i'm not absolutely positive i have nailed it (a bit more time will tell -- i'm keeping an eye on it

Re: [galaxy-dev] how to use projects for fair-share on compute-cluster

2012-01-13 Thread Edward Kirton
correction: i didn't adequately test what happens if the user_proj_map_db was not defined in the universe file; here's the changes: 157 # BEGIN ADD USER'S PROJ 158 try: 159 conn = sqlite3.connect(self.app.config.user_proj_map_db) 160 c = conn.cursor() 161

Re: [galaxy-dev] Getting global name 'copy_sample_loc_file' is not defined error when trying to install tool

2012-01-13 Thread Greg Von Kuster
I've corrected this problem in change set 6510:3d9f0ce7bb61, which is running on both the Galaxy main and test tool sheds. Thanks for reporting this issue. Greg Von Kuster On Jan 11, 2012, at 5:10 PM, Anthonius deBoer wrote: Im trying to install a tool from the toolshed that showed me this

[galaxy-dev] How to use scripts/api/update.py?

2012-01-13 Thread Carlos Borroto
Hi, I'm trying to use the update.py script and is not clear for me what to use for 'url' in the usage line: usage: create.py key url [key=value ...]. Which I'm guessing is just a carry over from create.py. I tried passing the direct link to the dataset: $ ./update.py my_key