global base path for shed_upload include relative paths #160
Description
I'm trying to replace a manual process for preparing tar-balls to push to the Tool Shed, however by using a common top level test-data/ (and tool-data/) folder this is harder than expected.
Current manual process as documented in this tool's README file:
$ tar -czf venn_list.tar.gz tools/venn_list/README.rst tools/venn_list/venn_list.* tools/venn_list/tool_dependencies.xml test-data/magic.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta
$ tar -tzf venn_list.tar.gz
tools/venn_list/README.rst
tools/venn_list/venn_list.py
tools/venn_list/venn_list.xml
tools/venn_list/tool_dependencies.xml
test-data/magic.pdf
test-data/venn_list.tabular
test-data/rhodopsin_proteins.fasta
I have been able to get the desired output (ignoring the order, #159) with a complicated .shed.yml entry like this:
include:
- source: README.rst
destination: tools/venn_list/README.rst
- source: venn_list.py
destination: tools/venn_list/venn_list.py
- source: venn_list.xml
destination: tools/venn_list/venn_list.xml
- source: tool_dependencies.xml
destination: tools/venn_list/tool_dependencies.xml
- source: ../../test-data/magic.pdf
strip_components: 2
- source: ../../test-data/venn_list.tabular
strip_components: 2
- source: ../../test-data/rhodopsin_proteins.fasta
strip_components: 2
Giving:
$ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/venn_list
cp /tmp/tmpybJqwL shed_upload.tar.gz
(.venv)[galaxy@ppserver planemo]$ tar -tzf /tmp/tmpybJqwL
tools/
tools/venn_list/
tools/venn_list/venn_list.py
tools/venn_list/tool_dependencies.xml
tools/venn_list/README.rst
tools/venn_list/venn_list.xml
test-data/
test-data/rhodopsin_proteins.fasta
test-data/magic.pdf
test-data/venn_list.tabular
I would like to use something along these lines in the .shed.yml file:
#All include paths from two levels up (i.e. prefix with ../../ to find the file)
include_offset: 2
include:
- tools/venn_list/README.rst
- tools/venn_list/venn_list.py
- tools/venn_list/venn_list.xml
- tools/venn_list/tool_dependencies.xml
- test-data/magic.pdf
- test-data/venn_list.tabular
- test-data/rhodopsin_proteins.fasta