[galaxy-dev] access system variables in tool xml (Matthias De Smet)

Others might have responded to this, and I can't remember the very latest approach, but I used the approach below... Its not easy though since api is read via script [BTW, topically, I still need on a regular basis!], but is passed over to command line app securely via a . For error situation

Re: [galaxy-dev] Importing workflows via command-line/Docker script

Thanks for the quick response Marius and Bjoern, really appreciate the help! Since I need to make this work in the next day or so, would you be interested in seeing what my script looks like Bjoern? I imagine it¹ll only be a couple of lines though to do this. Thanks again, Cam On 27/01/2016

Re: [galaxy-dev] Importing workflows via command-line/Docker script

Hi Cam, this would be possible using bioblend ( https://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html?highlight=workflow#module-bioblend.galaxy.workflows). Take a look at the `import_workflow_from_local_path` function. You'll need to have galaxy running for this (same as for

Re: [galaxy-dev] Importing workflows via command-line/Docker script

Sure, if you are fast we can include this in the galaxy-stable:16.01 release which will be release very soon. You can also create a PR against the 16.01 branch on: https://github.com/bgruening/docker-galaxy-stable/tree/16.01 Ciao, Bjoern Am 27.01.2016 um 09:22 schrieb Cameron Jack: > Thanks for

Re: [galaxy-dev] Importing workflows via command-line/Docker script

Hi Cam, as Marius already pointed out this is easily possible with bioblend. I would create a small script that takes the path to the GA file as input, preferably also a URL, and populates this in Galaxy. I would be interested to include such a script in the Main Docker container, so everyone

Re: [galaxy-dev] Retain the dbkey specified for an input dataset through a Galaxy workflow?

I’ve submitted an issue about this here: https://github.com/galaxyproject/galaxy/issues/1598 > On Jan 26, 2016, at 8:15 AM, Greg Von Kuster wrote: > > I’ve tracked down how the dbkey is getting lost on tool output datasets that > are part of a collection, but now I’m

Re: [galaxy-dev] Filtering dynamic options in tool with tagset

No worries. Although it is 'deprecated' it will be not be removed until we have a good alternative. On Wed, Jan 27, 2016 at 4:36 AM, Matthias De Smet wrote: > So it seems it has been deprecated a bit prematurely. Maybe the Galaxy > team should “undeprecate” it untill a

Re: [galaxy-dev] BED12 Data Format

Thanks for the info Dan. I've explored using bed12, but I have a few questions. 1. When attempting to use 'bed12' or 'Bed12' as a file type in a test, I get the following error: Exception: {u'message': {u'type': u'error', u'data': {u'file_type': u"An invalid option was selected for

Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

Thanks for the detailed breakdown of the places to check, Carl! I was able to fix the issue following the steps you've outlined. For the benefit of other readers, here is what I did to fix it: On Tue, Jan 26, 2016 at 10:09 AM, Carl Eberhard wrote: > Hi, Oksana > > There

[galaxy-dev] Filtering dynamic options in tool with tagset

Hi All, I’m trying to implement a tool that get a list of options through the “dynamic_options” tag. I try to filter the options that get returned with another param, but it doensn’t seem to work. my tool xml looks like this from the archive to a data library test.sh > $log

Re: [galaxy-dev] Filtering dynamic options in tool with tagset

Hi Hans-Rudolf Thanks again, you’re a lifesaver! Any suggestions on how I could eliminate the tag, as the wiki states it’s deprecated? I checked out but don’t see a straightforward wau to get the same results. Matthias > Op 27 jan. 2016, om 10:20 heeft Hans-Rudolf Hotz het

Re: [galaxy-dev] Filtering dynamic options in tool with tagset

So it seems it has been deprecated a bit prematurely. Maybe the Galaxy team should “undeprecate” it untill a viable alternative is found. Anyway, thanks again! Matthias > Op 27 jan. 2016, om 10:33 heeft Hans-Rudolf Hotz het volgende > geschreven: > > > > On 01/27/2016 10:29

[galaxy-dev] access system variables in tool xml

Hi again I’m trying to create a tool that interacts with galaxy through the API. For this, I need to get the users API key (or equivalent) en the domain name of the Galaxy host. The purpose of this tool is to get data and put it in a data library, so I suppose I need to use the API. Or is