Obtaining a tools.yaml to create a new galaxy docker flavour

Question: Obtaining a tools.yaml to create a new galaxy docker flavour

17 months ago by

colindaven • 0 wrote:

Hi,

we are running the galaxy-rna-workbench docker galaxy which is very nice.

We would like to extend this with new tools and especially data-managers and later workflows.

In this document ( we're not using GKS quite yet) its documented how you can create a tools.yaml file from an existing well configured galaxy instance. https://artbio.github.io/GalaxyKickStart/installing%20tools%20and%20workflows/#obtaining-a-tool_listyml-file

However, we do not have admin api key level access to any big Galaxy, eg. Galaxy main.

Is there any way to generate or find tools.yaml files from an existing "big" Galaxy instance ?

Thanks, Colin

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modified 17 months ago by Bjoern Gruening ♦ 5.1k • written 17 months ago by colindaven • 0

17 months ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi Colin,

just to be sure, you want to create a new Galaxy flavor (Docker image) based on-top of the RNA workbench or do you want to install all tools from the RNA workbench into a big Galaxy instance, independent of Docker?

For your last question we have here a small script for you: https://github.com/galaxyproject/ephemeris/blob/master/ephemeris/get_tool_list_from_galaxy.py

Cheers,

Bjoern

ADD COMMENT • link written 17 months ago by Bjoern Gruening ♦ 5.1k

Hi Björn,

I want to do the first option, to extend a Galaxy flavour.

I think I can solve it myself, using the api.

From this link I can get a JSON of the tools, then hopefully convert to yaml with a Python script https://usegalaxy.org/api/tools

Thanks for your help, Colin

ADD REPLY • link written 17 months ago by colindaven • 0

Colin, the link I posted above produces a yaml for you already.

ADD REPLY • link written 17 months ago by Bjoern Gruening ♦ 5.1k

Hi Björn. Ok, unfortunately I can't get it to work.

/data/rcug/galaxy_docker_preprot/tool_lists/ephemeris/ephemeris$

ls

common_parser.py generate_tool_list_from_ga_workflow_files.py __init__.py setup_data_libraries.py sleep.py common_parser.py.bak get_tool_list_from_galaxy.py run_data_managers.py shed_install.py workflow_install.py

rcug@hpc01:/data/rcug/galaxy_docker_preprot/tool_lists/ephemeris/ephemeris$

python get_tool_list_from_galaxy.py

Traceback (most recent call last): File "get_tool_list_from_galaxy.py", line 12, in <module> from .common_parser import get_common_args ValueError: Attempted relative import in non-package

By the way alternative installation over

conda install ephemeris

does not find the package on my systems despite being documented here.

conda install ephemeris Fetching package metadata ...............

PackageNotFoundError: Package missing in current linux-64 channels: - ephemeris Close matches found; did you mean one of these? ephemeris: ephem

ADD REPLY • link modified 17 months ago • written 17 months ago by colindaven • 0

pip install ephemeris should work.

ADD REPLY • link written 17 months ago by Bjoern Gruening ♦ 5.1k

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