Re: [galaxy-dev] Dataset collection generation from a tool

o do though. > > -John > > On Wed, Nov 12, 2014 at 4:25 PM, Aaron Petkau > wrote: > > I think I may have just found the answer to my question in this trello > card > > > https://trello.com/c/ndVQmt3G/1857-tools-should-be-able-to-generate-one-or-more-dataset-collections &g

Re: [galaxy-dev] Dataset collection generation from a tool

I think I may have just found the answer to my question in this trello card https://trello.com/c/ndVQmt3G/1857-tools-should-be-able-to-generate-one-or-more-dataset-collections On Wed, Nov 12, 2014 at 3:15 PM, Aaron Petkau wrote: > Hello, > > Does anyone know if it's possible

[galaxy-dev] Dataset collection generation from a tool

Hello, Does anyone know if it's possible to generate as output from a tool a dataset collection when it's input is only a single file? I'm imagining a tool which takes as input a file containing a list of URLs for files outside of Galaxy and generates as output a dataset collection that can then

[galaxy-dev] Galaxy Data Sources and Dataset Collections

Hello, I've been spending a bit of time looking over Data Sources for Galaxy. I've been thinking about designing a tool in Galaxy, similar to a Data Sources tool, which would take as input a file defining a list of URLs to import into Ga

Re: [galaxy-dev] Jobs stuck in "new" state - Data Library datasets to blame?

Are you attempting to upload datasets to a Data Library, and then copy to a history and run jobs on them right away? I've run into issues before where if I attempt to run a job on a dataset in a library before it is finished being uploaded and processed, then the job gets stuck in a queued state a

Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

Hmmm... you know what. I tested this out and it looks like Galaxy expects the git repo to be named the same as the package name in your tool dependencies file ffp-phylogeny. If you change the git command to: git clone https://github.com/apetkau/ffp-3.19-custom.git *ffp-phylogeny* I think it sho

Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

Hey Damion, You should be able to do *./*configure --disable-gui ... to get it to work (that is, make sure the full path to the configure command is given). At least I think that's probably what's going on. Aaron On Fri, Aug 1, 2014 at 12:32 PM, Dooley, Damion wrote: > Hi folks, > > Having a

Re: [galaxy-dev] Once-run galaxy archives

a cron/CI job and have it email you whenever it's run to say >> "hey, associate the branch/trigger a build" >> >>Cheers, >>> Bjoern >>> >>>>One downside to docker is that you need to get it installed on your >>>>

Re: [galaxy-dev] Once-run galaxy archives

daily.tgz). Would that work > for your use case as well? > > Eric > > On 07/21/2014 03:02 PM, Aaron Petkau wrote: > > Hello Eric, > > > > Your right about that, downloading the archive, installing all the eggs, > > and then updating the database takes a bi

Re: [galaxy-dev] Once-run galaxy archives

Hello Eric, Your right about that, downloading the archive, installing all the eggs, and then updating the database takes a bit of time (especially if you're like me and like re-running tests on nearly every change you make :P). I think it would be cool to have a pre-package Galaxy for integratio

Re: [galaxy-dev] Once-run galaxy archives

Hello Eric, I think that's a great idea. You may be interested in checking out Björn's Galaxy Docker image https://github.com/bgruening/docker-recipes/tree/master/galaxy which is very similar to what you're describing. A few other testing frameworks, like Galaxy bootstrap https://github.com/jmch

Re: [galaxy-dev] Tool dependency environments with functional tests

o source $i; done sh run_functional_tests.sh -installed Not sure if it's the best way to handle things, but it works for now. Aaron On Fri, Jul 11, 2014 at 2:54 PM, Aaron Petkau wrote: > Hello everyone, > > I've been trying to get some functional tests developed for my tools and > I'

[galaxy-dev] Tool dependency environments with functional tests

Hello everyone, I've been trying to get some functional tests developed for my tools and I'm trying to figure out how to properly run them. I'm following the guide at https://wiki.galaxyproject.org/TestingInstalledTools but when I run the functional tests against tools installed from my tool she

Re: [galaxy-dev] Workflows with Conditionals and Loops

I remember this being mentioned in a project called Tavaxy http://www.biomedcentral.com/1471-2105/13/77, but it's a separate piece of software (using Galaxy) and I don't know if it's been updated in a while so it may not be as useful for you. Not sure if anybody else had any experience with it? I

Re: [galaxy-dev] Galaxy command line API information

Hello Benoît, I remember seeing projects trying to do something similar (store workflows internally and execute on Galaxy), like http://refinery-platform.org/, so it could be useful to take a look there too. I've been trying to do something similar but with the Java interface to the Galaxy API ht