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

Hello Eric, That sounds like a pretty good idea. If there was a pre-built image available for whatever release I wanted to test against I could just cache it and (hopefully) get my tests running a bit faster. I'm not sure if anyone else is already doing this? Also, I remember there being mentio

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

Hi Aaron, Yeah, absolutely understandable. I want my tools tested early and often. I abuse my CI server for everything, especially for building and packaging software. In this case I was imagining that I might have it produce an archive on every tagged release, as well as producing a "daily" arch

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

Hi Aaron,Good points, I was considering using galaxy bootstrap. This is mostly for the CI folk who want to download an archive, unpack it, and be ready to install/test their tools. The hg clone and egg/db steps seem like unnecessary overhead for this specific use case.Cheers,Eric __

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

[galaxy-dev] Once-run galaxy archives

Currently the checkout options consist of hg clones, and archives that mercurial produces.  Having pulled or cloned galaxy a few times lately, I'm wondering if anyone would have a use for a once-run galaxy instance in an archive? I.e., I'd clone, run once to grab eggs and do the db migration, then

Re: [galaxy-dev] XML/json code to parse/get/create wrapper files to/from galaxy

Very cool, I will give it a try :) Am 21.07.2014 16:27, schrieb Rémy Dernat: Hi, I created a little repository on github to parse or create wrapper files. I have not implemented everything, but it is a good base, i.e. if you want to create a galaxy wrapper from a standard help output ! Just cl

Re: [galaxy-dev] Customizing the HTML datatype and altering the behavior of "download results" link.

Hi Peter, Thanks for the help. I managed to do what I wanted by subclassing the Html datatype, defining it as composite and overriding _archive_composite_dataset to link to the pre-packaged zip file. Defining it as composite was necessary as "html" seems to be treated specially in display_data()

Re: [galaxy-dev] getting API key from user/pass

Done. On Mon, Jul 21, 2014 at 10:30 AM, Eric Rasche wrote: > Martin, > > Ah, good to have the API call needed. Could this possibly be added to the > wiki, perhaps on Learn/API ? > > That particular URL doesn't seem to be in blend4j so this answers that

Re: [galaxy-dev] getting API key from user/pass

Martin,Ah, good to have the API call needed. Could this possibly be added to the wiki, perhaps on Learn/API?That particular URL doesn't seem to be in blend4j so this answers that question as well, thanks!Cheers,Eric21.07.2014, 15:13, "Martin Čech" : file  api/authenticate.py clas

[galaxy-dev] XML/json code to parse/get/create wrapper files to/from galaxy

Hi, I created a little repository on github to parse or create wrapper files. I have not implemented everything, but it is a good base, i.e. if you want to create a galaxy wrapper from a standard help output ! Just clone it and have fun : git clone https://github.com/remyd1/XMLparser-wrapper.git

Re: [galaxy-dev] getting API key from user/pass

file *api/authenticate.py* class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ): @web.expose_api_anonymous def get_api_key( self, trans, **kwd ): """ def get_api_key( self, trans, **kwd ) * *GET /api/authenticate/baseauth* returns an

[galaxy-dev] getting API key from user/pass

John, I'm looking to use blend4j, and I was wondering if there was a way to obtain the user's API key from a username/password pair? Cheers,Eric -- Eric RascheProgrammer IICenter for Phage TechnologyTexas A&M UnivesityCollege Station, TX 77843Ph: 4046922048   ___

Re: [galaxy-dev] Galaxy+Toolshed Docker image?

Hi Kyle, not that I know of, but I'm interested in adding such a feature on top of the base galaxy image. You can find the Dockerfile here: https://github.com/bgruening/docker-recipes Ciao, Bjoern Am 21.07.2014 15:39, schrieb Kyle Ellrott: I know there is a base docker image for Galaxy stab

[galaxy-dev] Galaxy+Toolshed Docker image?

I know there is a base docker image for Galaxy stable ( https://registry.hub.docker.com/u/bgruening/galaxy-stable/), but is there a docker image that will start both a server and a toolshed sever and link them? I was hoping that I could use something like that for testing shed based tool deployment

Re: [galaxy-dev] writing datatypes

Hi John, The general question, I think, is whether reproducibility is important. If it is, then we should not introduce new behavior that adversely impacts it. There are undoubtedly scenarios where reproducibility is not currently absolutely guaranteed, but those area of weakness should be co

Re: [galaxy-dev] writing datatypes

Please see my comments below. On Jul 20, 2014, at 3:22 PM, Peter Cock wrote: > On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning wrote: >> Hi, >> >> single datatype definitions only work if you haven’t defined any converters. >> Let's assume I have a datatype X and want to ship a X -> Y converter

Re: [galaxy-dev] writing datatypes

Hi, single datatype definitions only work if you haven’t defined any converters. Let's assume I have a datatype X and want to ship a X -> Y converter (Y -> X is also possible), we will end up with a dependency loop, or? The X repository will depend on the Y repository, but Y is depending on X

[galaxy-dev] bugs with relative path in library_import_dir

Hi, when you specify a library_import_dir in universe_wsgi.ini with a path relative to galaxy-dist, i.e. a directory: /home/galaxy/galaxy-dist/uploads is specified as: library_import_dir = uploads and you then try to Upload directory of files, everything's reported as fine, but you end up wit