Re: [galaxy-dev] Tool param type "library_data" (Dooley, Damion)

I understand a new tool form module is rolling out in the next few weeks. Will anything change in the HTML hidden input submit fields? Right now tool forms have the equivalent of: ... and then on to the visible fields. Cu

Re: [galaxy-dev] Parallelism using metadata

Hey Marco, Thanks for the e-mail. This is an awesome idea, but I am worried it is very hard to do this well in Galaxy. If you create symbolic links to the original file - then Galaxy might delete the original file and the derived files would all break without warning. Galaxy does have this separat

[galaxy-dev] The March 2015 Galaxy News

Hello all, As always, it's a busy time in the Galaxy . The March 2015 Galaxy News is out, and it's chock full of information. Here are some of the highlights. *UseGalaxy.org Update

Re: [galaxy-dev] Interested in GSOC idea "Docker Swarm and Compose" & ask for advices.

Our full trello board can feel somewhat overwhelming so have a look at this card with the easiest ways to contribute: https://trello.com/c/eFdPIdIB/1773-easiest-ways-to-contribute Martin On Mon, Mar 2, 2015 at 11:23 AM Björn Grüning wrote: > Hi Afe, > > it's usually a good idea to search for is

Re: [galaxy-dev] Interested in GSOC idea "Docker Swarm and Compose" & ask for advices.

Hi Afe, it's usually a good idea to search for issues that needs to be solved or some features that are missing. A good start for example is the Galaxy Trello board: https://trello.com/b/75c1kASa/galaxy-development The issue tracker of tools-iuc or tools-devteam: https://github.com/galaxyproject

[galaxy-dev] gatk tool config file

Hello, I would like to add a very simple GATK wrapper to galaxy, but I am facing one problem. When you want to use UnifiedGenotyper tool, the extension of the bam file must be .bam, and when you upload something to galaxy it changes its extension,is there any way to change this extension? or is it

Re: [galaxy-dev] gatk tool config file

On Mon, Mar 2, 2015 at 4:08 PM, Roberto Alonso CIPF wrote: > Hello, > > I would like to add a very simple GATK wrapper to galaxy, but I am facing > one problem. When you want to use UnifiedGenotyper tool, the extension of > the bam file must be .bam, and when you upload something to galaxy it > ch

[galaxy-dev] Authentication failed when pushing to tool shed

Hello, I’m trying to install a tool shed and I’m having an issue when pushing a tool on it. The authentication to both Galaxy and Galaxy tool shed is handled by Apache through a LDAP. I can access the tool shed interface, create repository and clone it without problem. I can even upload files

[galaxy-dev] Galaxy Update Problem

Hi all, I installed my Galaxy instance from https://bitbucket.org/galaxy/galaxy-dist/. But I did not use Mercurial to install Galaxy at that time, because I was not farmiliar with Mercurial and failed severed times. The instance imported many tool kits later, as it would be very difficult to r

[galaxy-dev] Parallelism using metadata

Hello Galaxy Dev, I have a question regarding parallelism on a BAM file. I have currently implemented 3 split options for the BAM datatype 1) by_rname -> splits the bam into files based on the chromosome 2) by_interval -> splits the bam into files based on a defined bp length, and does so acros

[galaxy-dev] Please post a Galaxy vacancy at the University of Oslo

Opening @ University of Oslo The University Center for Information Technology (USIT) at the University of Oslo has an opening for a developer / bioinformatician