Question: Command line update for tool dependencies
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gravatar for lachlan.simpson
3 months ago by
lachlan.simpson10 wrote:

When installing Galaxy, we run an ansible playbook that does most of the heavy lifting. I particularly like the ephemeris based automagic tool installation:

shed-tools install --api_key "deepsecret" -t /galaxy/development/config/tool_list.yaml --galaxy "http://localhost/galaxy/" --install_resolver_dep

When I go to Manage Tools in the Admin interface, there is a pleasingly long list of green/installed markers.

However, what I find is that not all dependencies are installed. When I go to the page Manage Tool Dependencies, there are a number of listed tools with dependencies that aren't installed.

https://host/galaxy/admin/manage_tool_dependencies

What is the command line instruction to fix this (ie, look down the list, find those with a red cross, check the appropriate box and click "Install checked dependencies using Conda"). I'm sure there's an easier programmable way than having to do it like this?

dependenciess tools • 72 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by lachlan.simpson10
0
gravatar for lachlan.simpson
3 months ago by
lachlan.simpson10 wrote:

When I watch the logs I see some lines that look like this:

 Executing command: /galaxy/development/database/dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --channel r --name __rpy2@2.7.8 rpy2=2.7.8

Is that how we can update them? How do I find the list of names to go in --name? Also, which env do I run it in - or does calling that particular conda binary have/provide all the env details I need.

ADD COMMENTlink written 3 months ago by lachlan.simpson10
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