Re: [galaxy-dev] Workflow bug when *.loc entries are missing

2015-04-01 Thread Peter Cock
On Tue, Mar 31, 2015 at 6:12 PM, John Chilton wrote: > I think it is probably a pair of bugs you are seeing: > Having tried the revert, yes, I think so too. > The wrong database being selected is probably this: > https://trello.com/c/72WuZ8mu. It would be interesting to know if > reverting this

Re: [galaxy-dev] Workflow bug when *.loc entries are missing

2015-04-01 Thread Saket Choudhary
On 1 April 2015 at 02:06, Peter Cock wrote: > On Tue, Mar 31, 2015 at 6:12 PM, John Chilton wrote: >> I think it is probably a pair of bugs you are seeing: >> > > Having tried the revert, yes, I think so too. > >> The wrong database being selected is probably this: >> https://trello.com/c/72WuZ8m

Re: [galaxy-dev] Workflow bug when *.loc entries are missing

2015-04-01 Thread Peter Cock
On Wed, Apr 1, 2015 at 11:29 AM, Saket Choudhary wrote: > On 1 April 2015 at 02:06, Peter Cock wrote: >> On Tue, Mar 31, 2015 at 6:12 PM, John Chilton wrote: >>> I think it is probably a pair of bugs you are seeing: >>> >>> ... >>> >>> The fix unfortunately is messy and will likely break stuff.

Re: [galaxy-dev] Using synchronous method to upload multiple files

2015-04-01 Thread Daniele P Colobraro
Thanks John for your help, if I get it will I set just a external view of my files? My idea is to provide multiple files in the galaxy history. I tried to rewrite the 'galaxy.joson' file but without results. So far, I have made up just the tool below: upload3.py $report1 $report1.id $__new_file_p

Re: [galaxy-dev] storing "set max value" in trackster for wig file display

2015-04-01 Thread Jeremy Goecks
Hi Hans, Sorry for the slow reply. Please go ahead and create a card so this issue doesn’t get lost. IIRC, one challenge here is that fixing the min/max can lead to weird views when you move around the genome where the min/max changes. I think this was the original reason that max (and min?) we

[galaxy-dev] Installing workflows from the Tool Shed is very confusing

2015-04-01 Thread Peter Cock
Hello all, I've been playing with the Tool Shed lately for publishing Galaxy workflows - and realised the download process is still very complicated, especially the final hurdle - importing the workflow in order to actually use it. For the following example I am starting from a clean state - an a

Re: [galaxy-dev] Trouble maintaining Galaxy config on cloud instance

2015-04-01 Thread David Kovalic
Enis, Thanks for the pointers, I tried this and it didn't work for me. After I modified *cm/util/galaxy_conf.py *CM would no longer successfully start up my cluster. I suspect user-induced-syntax-error at my end when I modified the file, I am a perl guy and my python is not so great :( What I did

Re: [galaxy-dev] dat quota

2015-04-01 Thread Dannon Baker
Hey Charles, This was an error on our end (bug that has since been fixed), and I've recalculated your quota. You should be good to go now. Thanks for using Galaxy! -Dannon On Thu, Mar 26, 2015 at 8:21 AM, Williams, Charles Houston < charles.williams...@vanderbilt.edu> wrote: > > After readin

[galaxy-dev] Multiple outputs of unknown types

2015-04-01 Thread David Kelly
Hello, I've looked through the documentation about tools that produce multiple output files, but it seems like you're required to know the data types ahead of time (or make assumptions based on input data). But what about a case where you don't know what the output datatypes will be? Is it just po