Re: [galaxy-dev] S3/Swift object store cache path and `extra_dir`s

2015-02-20 Thread Brian Claywell
Hi Dannon, I'm stoked that Charles's PR made it into master -- thanks! Have you had a chance to look into the job_work and temp extra_dir issue? Please let me know if there's anything I can do to help out! Cheers, Brian On Mon, Feb 9, 2015 at 1:39 PM, Dannon Baker wrote: > Hey Brian, > > Th

Re: [galaxy-dev] (no subject)

2015-02-20 Thread Briand, Sheldon
Hi, user galaxy; worker_processes 1; #error_log logs/error.log; #error_log logs/error.log notice; #error_log logs/error.log info; #pidlogs/nginx.pid; error_log /var/log/nginx/error.log info; pid/var/run/nginx.pid; events { worker_connections 1024; } http { in

Re: [galaxy-dev] (no subject)

2015-02-20 Thread John Chilton
I am not sure what the problem is - any chance you can share your nginx configuration file? On Fri, Feb 20, 2015 at 1:13 PM, Briand, Sheldon wrote: > Hi, > > > > I’m seeing the following error when trying to use upload file with a local > file that is larger than 8Kb: > > > > galaxy.web.framework

[galaxy-dev] (no subject)

2015-02-20 Thread Briand, Sheldon
Hi, I'm seeing the following error when trying to use upload file with a local file that is larger than 8Kb: galaxy.web.framework.decorators ERROR 2015-02-19 16:51:48,280 Uncaught exception in exposed API method: Traceback (most recent call last): File "/BigData/galaxy/galaxy-dist/lib/galaxy/

Re: [galaxy-dev] biopython installation

2015-02-20 Thread Peter Cock
On Fri, Feb 20, 2015 at 3:56 PM, Lapointe, David wrote: > I tried installing biopython and dependancies from the toolshed but this > does not seem to be functional even though these tools say INSTALLED. How are you testing it? Any Galaxy copy of Biopython will not be available to the system Pytho

[galaxy-dev] biopython installation

2015-02-20 Thread Lapointe, David
I tried installing biopython and dependancies from the toolshed but this does not seem to be functional even though these tools say INSTALLED. Is there something that I should do that I missed? I sis better to installed them in the regular python fashion? -- David Lapointe Ph.D. Sr. Bioinforma

Re: [galaxy-dev] problem with latest toolshed devteam cuffmerge wrapper multi-select

2015-02-20 Thread Nicola Soranzo
Hi Nikhil, I would suggest to open an issue on https://github.com/galaxyproject/tools-devteam/issues Best, Nicola Il 20.02.2015 10:28 Nikhil Joshi ha scritto: > So I am doing some debugging and it looks like in the from_html function in the SelectToolParameter class, it gets the legal values

Re: [galaxy-dev] problem with latest toolshed devteam cuffmerge wrapper multi-select

2015-02-20 Thread Nikhil Joshi
So I am doing some debugging and it looks like in the from_html function in the SelectToolParameter class, it gets the legal values for the build using the get_legal_values function. This returns the correct values when I choose only one gtf file, but when I choose multiple gtf files the list of le