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Manifests can point at local test-data folders now #150

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peterjc
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@peterjc peterjc commented Dec 6, 2022

As of #149, each tool has its own test-data/ folder (currently a symlink to the top level shared folder). This means the manifest no longer needs to point at the top level folder.

$ sed -i.bak "s#../../test-data/#test-data/#g" tools/*/.shed.yml

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I would suggest to do this 1 PR per tool / tool collection. There will probably to many lint and test errors to keep it manageable, or?

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peterjc commented Dec 6, 2022

I think the strip components setting would explain the otherwise mystifying errors like this:

ValueError: Destination for 'test-data/four_human_proteins.fasta' should be a full filename!

As of #149, each tool has its own test-data/ folder
(currently a symlink to the top level shared folder).
This means the manifest no longer needs to point at
the top level folder.

$ sed -i.bak "s#../../test-data/#test-data/#g" tools/*/.shed.yml
This was sensible for consistency with the top-level
shared tool-data and test-data folders, but we're
phasing that out to follow IUC standard layout
Now using per-tool sub-folders as per IUC recommended layout.
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peterjc commented Dec 6, 2022

Seems 940f223 has not worked to skip problematic tests...

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