Re: [galaxy-dev] Failed to generate job destination

Hi John, please find attached my jobs_conf.xml file. I was not able to find any systematic in that error. It seems to happen not so often. Thanks, Bjoern > Hey Bjoern, > > Can you post your job_conf.xml or send it to galaxy-b...@bx.psu.edu > if it has something sensitive in it, alternatively

Re: [galaxy-dev] Failed to generate job destination

Hey Bjoern, Can you post your job_conf.xml or send it to galaxy-b...@bx.psu.edu if it has something sensitive in it, alternatively your runner urls if you are still using the older format for specifying these things? Is this for every job or just certain tools? -John On Thu, Nov 14, 2013 at 5:

[galaxy-dev] Failed to generate job destination

Hi, anyone has seen the following bug in Galaxy November release? galaxy.jobs.handler ERROR 2013-11-15 00:07:41,008 Failed to generate job destination Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 311, in __check_if_ready_to_run se

Re: [galaxy-dev] Errors running DRMAA and PBS on remote server running Torque 4

Carrie, This turned out to be an issue with Torque 4 changing from pbs_submit() to submit_pbs_hash() procedure while both pbs-drmaa and pbs-python were still using pbs_submit(). The maintainer of the pbs-drmaa library (http://sourceforge.net/p/pbspro-drmaa/wiki/Home/ ) Mariusz Mamonski provided

[galaxy-dev] Setting a queue for torque submission

Hello, I am going to move your question over to the galaxt-...@bx.psu.edu mailing list to give it better visibility to the development/local install community. http://wiki.galaxyproject.org/MailingLists#The_lists I didn't find it over here already, but apologies if double posted. Also, since I

[galaxy-dev] wiki contributions: Admin/Config/ProFTPd_with_AD

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I'd like to contribute what I've learnt today to this particular page. As it is "locked", I am unsure how to contribute my information, so I'm posting here in the hopes that someone with rights will update it. Formatted in (pandoc compatible) Markdown

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

If, by "current installation methods" you are not referring to Tool Shed repository installation methods for installing tool dependencies, then please read no further. For installing tool dependencies along with repositories from the Tool Shed, fabric is currently being used. However, it's bee

[galaxy-dev] Fwd: Managing Data Locality

Forgot to cc galaxy-dev on this, it is too riveting not to post :). -John -- Forwarded message -- From: John Chilton Date: Thu, Nov 14, 2013 at 10:00 AM Subject: Re: [galaxy-dev] Managing Data Locality To: "Paniagua, Eric" Hey Eric, Sorry for the delayed response, I have pu

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

On Nov 14, 2013, at 12:21 PM, Peter Cock wrote: > On Thu, Nov 14, 2013 at 5:13 PM, Nate Coraor wrote: >> Bash is easily obtained on these systems and I think the extra functionality >> available in post-Bourne shells ought to be allowed. I also question how >> many people are going to run tools

Re: [galaxy-dev] BAM/BAI index file test problem on (Test) Tool Shed

Hi Peter, On Nov 14, 2013, at 11:27 AM, Peter Cock wrote: > On Wed, Nov 13, 2013 at 12:03 PM, Greg Von Kuster wrote: >> Hello Peter, >> >> Yesterday we discovered what Björn has communicated and added it to the >> Trello card for this issue: >> >> https://trello.com/c/sN2iLCCn/99-bug-in-inst

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

On Thu, Nov 14, 2013 at 5:13 PM, Nate Coraor wrote: > Bash is easily obtained on these systems and I think the extra functionality > available in post-Bourne shells ought to be allowed. I also question how > many people are going to run tools on *BSD since most underlying > analysis tools tend to

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

Bash is easily obtained on these systems and I think the extra functionality available in post-Bourne shells ought to be allowed. I also question how many people are going to run tools on *BSD since most underlying analysis tools tend to only target Linux. That said, shell code should be restr

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

On Tue, Nov 12, 2013 at 3:33 AM, Dave Bouvier wrote: > Peter, > > Thanks for bringing this to our attention, we're working on fixing a number > of issues with the test framework, and hope to have more information for you > tomorrow. > > --Dave B. Hi Dave, Good news, the BLAST+ tests appear to h

Re: [galaxy-dev] BAM/BAI index file test problem on (Test) Tool Shed

On Wed, Nov 13, 2013 at 12:03 PM, Greg Von Kuster wrote: > Hello Peter, > > Yesterday we discovered what Björn has communicated and added it to the > Trello card for this issue: > > https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1 > > ... > > becomes the following in your renam

Re: [galaxy-dev] tardis job splitter

> Very interesting approach, thanks for reaching out and open sourcing your > stuff! thanks for your time having a look at this, and your comments and advice ! > > What form would this contribution take? Are there changes that need to be > made to the Galaxy core that need to be made or were yo

[galaxy-dev] Next GalaxyAdmins Meetup: November 20

Hello all, The next GalaxyAdmins meetup will be Wednesday, November 20, at 10am US Central time. See the meetup page for a link and directions for connecting to the meetup. *GCC2013 GalaxyAdmins BoF Followup* This is our