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 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 7:17 pm, "Björn Grüning" bjoern.gruening@gmail.com wrote:
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 can use this similar to the script for installing tools.
A second option would be to upload the workflow with all dependencies to the TS and than simply install the workflow.
Similar to this one:
https://github.com/bgruening/galaxytools/tree/master/workflows/ncbi_blast_ plus/find_three_genes_located_nearby
Hope this helps, Bjoern
Am 27.01.2016 um 03:14 schrieb Cameron Jack:
Hi all,
I've been developing a Dockerfile and repositories to enable users to set up an NGS forensics pipeline. So far so good, I can build the image (based on Bjoern Gruening's excellent galaxy-stable Docker image) and incorporate all the various tools I need, including custom ones with custom interfaces. I've also built some workflows within a running image and exported them to .ga files, but now I'm wondering if there is a way to import those back in to a new image via the Dockerfile? I'd rather have everything set up for the users upon building the image, rather than logging in as admin and then importing the workflow. Is this possible? If so, how?
Thanks for any and all answers.
Best regards,
Cam
Cameron Jack
Bioinformatician ANU Bioinformatics Consulting Unit The Australian National University
The John Curtin School of Medical Research Building 131 Garran Road Acton 0200, ACT
Ph (office): +61 2 612 51128 Ph (mobile): +61 4 2368 0745 Email: cameron.jack@anu.edu.au Group email: abc@anu.edu.au
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