Hi Steve,
are you fine restricting your tools to a recent Galaxy version, let's say 6 month old?
If you forget about tool_depenencies.xml files, completely forget these! Conda packaging is the way to go and way more easy for you.
Let me know and I will give a short introduction or follow the description on https://github.com/bioconda/bioconda-recipes to create a PR and a package for your tool.
This can be used by Galaxy automatically. Thanks, Bjoern
Am 14.07.2016 um 03:49 schrieb Steve Cassidy:
I’m just getting my head around tool dependencies and in doing so trying to push my tools to a local toolshed which I can handily run with the planemo/server docker image via Kitematic.
That toolshed is set up with an admin user planemo@test.commailto:planemo@test.com so I have a stanza in my .planemo.yml:
shed_username: "stevecassidy" sheds: http://localhost:32768/: key: "" email: "planemo@test.commailto:planemo@test.com" password: "planemo"
Now I try to create a repository in the toolshed with planemo:
$ planemo shed_create --shed_target http://localhost:32768/ Repository created cd '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git rev-parse HEAD cd '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git diff --quiet Repository [alveoimport] does not exist in the targeted Tool Shed.
Note the conflicting messages here. The repository is created (and I can confirm that it is there) but then I get the message that the repo does not exist in the Toolshed. After a bit of digging it turns out that this is because the repo is owned by the user ‘planemo’ rather than my username as declared in .planemo.yml. If I add —owner plane to the command then it works fine.
So I’m not sure if this is a bug in the shed_create code or a weird interaction with the setup on planemo/server.
Steve
— Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy
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