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Question: How to create groups of tools and properly establish their dependencies?
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gravatar for alexander.lenail
2.6 years ago by
alexander.lenail • 0
alexander.lenail • 0 wrote:

I now want to create another tool, in the same repository as the previous tool I made. So now that tool's directory looks like:

Contents:

chipsequtil/
    README.md
    map_to_known_genes/
        map_to_known_genes.py
        map_to_known_genes.xml
        tool_dependencies.xml
    pieplot_macs/
        pieplots_macs.py
        pieplots_macs.xml
        tool_dependencies.xml
    tool_dependencies.xml

The exterior tool_dependencies file specifies the actual dependencies. The inner ones are just "../tool_dependencies.xml". But when I go to upload the tar file, I get this error:

Exception attempting to parse /srv/toolshed/main/var/data/repos/002/repo_2257/chipsequtil/map_to_known_genes/tool_dependencies.xml: not well-formed (invalid token): line 1, column 2

So my question is: How should I go about creating two tools? Should they be in different repositories? How should I be specifying dependencies? Where can I find a tutorial that explains this?
software error • 739 views
ADD COMMENT • link •
modified 2.6 years ago by Bjoern Gruening ♦ 5.1k • written 2.6 years ago by alexander.lenail • 0
0
gravatar for Bjoern Gruening
2.6 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi Alex,

we recommend to only have one tool per TS repository. So this corresponds to uploading pieplot_macs and map_to_known_genes both with it's own tool_dependencies_xml file. Are you using planemo to upload tools to the TS? If so there are some nice feature that automatise tool development and pushing to TSs for you.

Cheers, Bjoern
ADD COMMENT • link written 2.6 years ago by Bjoern Gruening ♦ 5.1k

I'm not using Planemo. How does one create a group of tools then?

ADD REPLY • link written 2.6 years ago by alexander.lenail • 0

Use planemo ;) It's worth it! You need to learn a little bit at the beginning, but the documentation is very good and it helps you so much in debugging and testing.

ADD REPLY • link written 2.6 years ago by Bjoern Gruening ♦ 5.1k
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