[galaxy-dev] [patch] Job Runner Eggs

2011-01-11 Thread John Chilton
Hello, Currently lib/galaxy/config.py requires that custom job runners be paired with exactly one egg for fetching, this seems less than ideal since runners may need 0 eggs (as is the case for a runner I am implementing) or multiple eggs. Attached is a minor patch that addresses this. Ple

Re: [galaxy-dev] Easy download/setup of Bacterial Genbank and multiple alignment files from UCSC?

2011-01-11 Thread Paszkiewicz, Konrad
Hi all, Many thanks for that Peter. It worked a charm. There does seem to be a bug in there somewhere. If more than one item is selected for retrieval at a time, only a single item is returned. The other items all return a 'This file cannot be found' error. Finally as an aside, could this sy

Re: [galaxy-dev] remote user environment variable?

2011-01-11 Thread Hans-Rudolf Hotz
Hi David I'm trying to set up a mechanism to copy a local file using a setuid executable, based on whether the registered user has read access to the local file in question. Is there any means for a tool to know the registered user who is running it? you can use the variable "$userEmail"

[galaxy-dev] remote user environment variable?

2011-01-11 Thread David Hoover
I'm trying to set up a mechanism to copy a local file using a setuid executable, based on whether the registered user has read access to the local file in question. Is there any means for a tool to know the registered user who is running it? David Hoover Helix Systems Staff http://helix.nih.go

Re: [galaxy-dev] Recommendation for Grid/Cluster management ?

2011-01-11 Thread Chris Cole
On 10/01/11 22:27, Assaf Gordon wrote: Slightly off-topic, but for a new Galaxy installation - What would you recommend for a free (FOSS) Grid/Cluster management product ? SGE is not free any more (Oracle Grid Engine is "90-days evaluation, binaries only" free, starting 6.2u6). Ease of adminis

Re: [galaxy-dev] Recommendation for Grid/Cluster management ?

2011-01-11 Thread Haarst, Jan van
> -Oorspronkelijk bericht- > Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev- > boun...@lists.bx.psu.edu] Namens Assaf Gordon > Verzonden: Monday, January 10, 2011 11:27 PM > Aan: galaxy-...@bx.psu.edu > Onderwerp: [galaxy-dev] Recommendation for Grid/Cluster management ? > > S