Re: [galaxy-dev] Cannot run Galaxy : socket.gaierror: [Errno -2] Name or service not known

On 04/11/12 16:39, Marcelo Timmerman wrote: Nobody? Anyone knows if using nginx would avoid the internal HTTP Python server? It appears that nginx is used as a proxy in front of the Python/Paste server, not as a replacement. You could use something like mod_wsgi with Apache instead of that

Re: [galaxy-dev] Wrapping web-tools

On Mon, Nov 5, 2012 at 5:53 AM, Franco Caramia franco.cara...@petermac.org wrote: Hi list, I’m trying to find documentation or examples on how to wrap web-tools (like primer3, optimus primer) in Galaxy. Any useful links or examples would be of great help. Thanks, Franco I'm not

[galaxy-dev] Mapping tools

Hi I'm a new Galaxy user and last week managed to map some sequences, but since Thursday the jobs won't start, even when I try re-running the one ones I did last week Lee -- ___ Please keep all replies on the list by using reply all in your

Re: [galaxy-dev] phylotastic hackathon (Jan 28 - Feb 1, Tucson, AZ) of possible interest to galaxy developers

Arlin, this sounds great. There have been a few discussions on the list over the last two weeks about Phylogenetic tools, it would be great if the groups responsible could send representatives to the hackathon to coordinate. My group would definitely like to send at least one Galaxy core team

Re: [galaxy-dev] Cannot run Galaxy : socket.gaierror: [Errno -2] Name or service not known

On Nov 5, 2012, at 5:39 AM, Paul Boddie wrote: On 04/11/12 16:39, Marcelo Timmerman wrote: Nobody? Anyone knows if using nginx would avoid the internal HTTP Python server? It appears that nginx is used as a proxy in front of the Python/Paste server, not as a replacement. You could use

Re: [galaxy-dev] Where should I put a tool's required binaries?

Sorry for bumping this, but it seems like such a standard boilerplate step of installing a tool that someone muts know how. -Joel I installed the?bedtools tool from the public toolshed to my galaxy cluster. The jobs were failing because I hadn't installed the required binaries: ? ?An

Re: [galaxy-dev] Where should I put a tool's required binaries?

On Mon, Nov 5, 2012 at 5:34 PM, Joel Rosenberg thisisj...@hotmail.com wrote: Sorry for bumping this, but it seems like such a standard boilerplate step of installing a tool that someone muts know how. -Joel Personally I've just been installing them on the $PATH, typically under $HOME/bin of

Re: [galaxy-dev] Where should I put a tool's required binaries?

If you want to keep your tools separated by name and version (recommended) see the section Managed Tool Dependencies at http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies -- James Taylor, Assistant Professor, Biology/CS, Emory University On Mon, Nov 5, 2012 at 12:44 PM, Peter Cock

Re: [galaxy-dev] Where should I put a tool's required binaries?

Thanks Peter, I tried doing something similar, but there wasn't a location in the galaxy user's $PATH that would persist across a cluster reboot or could be snapshotted (like the tools or data volumes). Adding /mnt/galaxyTools/my_dep_binaries or something to the $PATH would work temporarily,

Re: [galaxy-dev] Where should I put a tool's required binaries?

On Mon, Nov 5, 2012 at 6:09 PM, Joel Rosenberg thisisj...@hotmail.com wrote: Thanks Peter, I tried doing something similar, but there wasn't a location in the galaxy user's $PATH that would persist across a cluster reboot or could be snapshotted (like the tools or data volumes). Adding

Re: [galaxy-dev] Dynamic job runner status? Could I use it in combination with job splitting?

On Fri, Nov 2, 2012 at 6:03 PM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote: Here is the blastn rule procedure code and the relevant snippet of the default runner procedure. I just added the database based multiplier, so this part is very simple at the moment. I just set a bogus multiplier of

Re: [galaxy-dev] Where should I put a tool's required binaries?

Thanks, James. That page is exactly what I was looking for. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists,

Re: [galaxy-dev] Unnamed histories proliferating, can't get to my data

Hi Amit, I'm not understanding the original process that results in the problem. You're attempting to upload a file (as an import from an FTP dir), but that file never appears in your current history, or any of your saved histories? --nate On Nov 1, 2012, at 8:48 PM, Karger, Amir wrote:

Re: [galaxy-dev] Dynamic job runner status? Could I use it in combination with job splitting?

On Nov 5, 2012, at 2:15 PM, Carlos Borroto carlos.borr...@gmail.com wrote: On Fri, Nov 2, 2012 at 6:03 PM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote: Here is the blastn rule procedure code and the relevant snippet of the default runner procedure. I just added the database based multiplier,

Re: [galaxy-dev] How to add the option -c enabled to the qsub command?

Thanks for the link, Scott, I've confirmed that setting the job runner as pbs://machine.name/queue.name/-l nodes=n:ppn=m -c enabled/ in universe_wsgi does not work. Luobin On Mon, Nov 5, 2012 at 10:30 AM, Scott McManus scottmcma...@gatech.eduwrote: I recommend checking out John Chilton's

[galaxy-dev] xgrid cluster computing

Hi Galaxy team, So our university has decided to switch our xgrid clusters back on and we are looking to set Galaxy up on these. Has anyone got (or tried) to set up Galaxy on xgrid before? xgrid supposedly conforms to DRMAA so technically Galaxy should work, correct? Cheers, Ed

[galaxy-dev] language inside command tag set

Hi, I'm looking for documentation on what I can do inside the command tag for tools. I know of things like #if str( $input ) == 'yes': Do stuff #end if can I do for loops? What should I google? I can't find anything on the wiki. Thanks, Kevin.