Re: [galaxy-dev] ProFTPD integration with Galaxy

2013-06-21 Thread Malcolm Tobias
Ricardo, I followed the advice you offered back-channel and backed off the galaxy changes to support pbkdf2. I can now authenticate via the latest stable release of ProFTPD. Thanks! Malcolm On Thursday 20 June 2013 10:54:44 Perez, Ricardo wrote: > I am sorry, i posted the wrong configuratio

[galaxy-dev] Styling the Galaxy tool config xml

2013-06-21 Thread graham etherington (TSL)
Hi, I'm trying to see if I can style Galaxy tools, so instead of all the input fields being a long list one after the other, I can align a few of the fields side-by-side. Has anyone any suggestions on how I might accomplish this? Best wishes, Graham Dr. Graham Etherington Bioinformatics Support O

Re: [galaxy-dev] Portable tool identifiers in workflows

2013-06-21 Thread Peter Cock
On Fri, Jun 14, 2013 at 1:40 AM, Greg Von Kuster wrote: > Hi Peter, > >> On Jun 13, 2013, at 4:14 PM, Peter Cock wrote: >> >>> On Thu, Jun 13, 2013 at 6:34 PM, Greg Von Kuster wrote: >>> >>> Hello Peter, >>> >>> Unfortunately, workflows are currently not very compatible with >>> the tool shed -

Re: [galaxy-dev] Tophat2 output issue on LWR runner

2013-06-21 Thread Nikos Sidiropoulos
Hi John Thank you for the reply. In the lwr_staging directory all the runs from tophat are kept in (separate folders for each run) which means that the job failed to finish. In the paster.log the most common error is HTTPNotFound: No file found with path lwr_staging//working/insertions.bed Tha

Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails

2013-06-21 Thread jean-François Taly
Thanks Dannon, I indeed managed to have the galaxy-central version installed. I already see some problems but I will open another thread if necessary. Regards the DB engine, this new Galaxy I am deploying now is only a toy server I want to use in the Galaxy meeting in Oslo. I would like to have

Re: [galaxy-dev] nglims roles

2013-06-21 Thread Brad Chapman
Lee; Glad the capitalization role change got things working smoothly for permissions. > I guess one more question for today. Our lab will be taking care of all > library preps and so we want to simplify and remove a few options including > Multiplexing/barcodes, library construction, and library

Re: [galaxy-dev] visulaization tool

2013-06-21 Thread shashi shekhar
Hi James, galaxy.pdb is a dataset  in  galaxy , which is shown by  this url   http://10.180.8.54:9098/display_application/1fad1eaf5f4f1766/jmol_pdb/jmol_main/5da8464cb811e1a6/data/galaxy.pdb. i want to download this link  in galaxy by using python or java . after downloading,downloaded file c

Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails

2013-06-21 Thread Dannon Baker
Hi Jean-François, The index issues preventing a new instance from starting are resolved in the stable branch of galaxy-central; if you pull updates from that branch you should be able to start a new instance. While the instance will start and run, there are other peculiarities I still need to res

Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails

2013-06-21 Thread jean-François Taly
Dear all, I am having the same problem as Linda with a fresh installation of version 20130603. In the thread of her mail Dannon Baker said : "That said, this doesn't resolve the mysql index issues, which I'm currently working on. I hope to have a fix for them available soon, though." I wou