User: lachlan.simpson

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10 months, 3 weeks ago
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l**************@petermac.org

Posts by lachlan.simpson

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Comment: A: 18.05 administration Charts: guerler or iuc
... Great - thanks. Just cleaning up our dev env I noticed that it hadn't installed properly and wanted to confirm I was replacing like with like. ...
written 8 weeks ago by lachlan.simpson10
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18.05 administration Charts: guerler or iuc
... Hi, in the [upgrade notes for 18.05][1] it states > The charts repository that powers Galaxy built-in visualizations that > need backend computation has been moved to the IUC account. In order > for these visualization options to keep working, admins need to > install the following repo ...
charts installation written 9 weeks ago by lachlan.simpson10
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Answer: A: Command line update for tool dependencies
... 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 ...
written 4 months ago by lachlan.simpson10
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Command line update for tool dependencies
... 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 ...
tools dependenciess written 4 months ago by lachlan.simpson10
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Automated Galaxy Installation: ephemeris or bioblend?
... I have been handed an Ansible playbook to install Galaxy given our specific requirements. I cannot speak to why the [sanctioned Ansible deployment script][1] wasn't used and don't really want to start a debate on that. I've almost got the homemade working, but it's failing at the end during tool in ...
bioblend ephemeris installation toolshed ansible written 4 months ago by lachlan.simpson10 • updated 4 months ago by Martin Čech ♦♦ 4.8k
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Source branch and tag difference?
... We are running our server off the v17.09 *tag* from the git repository. I note that it hasn't been updated since November 2017. The release_17.09 *branch* was updated last night. What is the organisational difference between the branch/tag naming structures in the galaxy source control system? ...
tag branch release galaxy git written 5 months ago by lachlan.simpson10 • updated 5 months ago by Jennifer Hillman Jackson25k
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Comment: A: Bioblend: should I update, how do I update?
... Martin, Thanks, that was the information I was after. ...
written 5 months ago by lachlan.simpson10
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Comment: A: Bioblend: should I update, how do I update?
... Thanks Jen. I should have been clearer in my question. 1. Is the proper place to update *within* galaxy's venv? (we have set that to be /path/to/galaxy/codebase/.venv) 2. Is it safe to do so - ie should I expect things to "just work" after the update? ...
written 5 months ago by lachlan.simpson10
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Bioblend: should I update, how do I update?
... I've just noticed that our Galaxy 17.09 installation has Bioblend 0.9 installed, and that one of the changes in Bioblend 0.10 was "support for galaxy 17.09". Actually, now that I've looked into how it was installed, I see that the virtualenv that's created when Galaxy is installed only has bioblend ...
bioblend upgrades written 5 months ago by lachlan.simpson10

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