Question: toolshed repository - "This revision can be installed: False" - why?
1
gravatar for esch0041
13 months ago by
esch004160
esch004160 wrote:

I built a tool that passed planemo test and planemo shed_lint, and I deployed it to a testtoolshed repository using planemo shed_create with the .shed.yml here.

When I look at it in the test toolshed w4mclassfilter the repository browser says "This revision can be installed: False".

w4mclassfilter does not come up in the results when I "Search for Valid Tools", and I am unable to find it to install into my Galaxy instance - which in of itself is no surprise since it is marked as uninstallable.

Why is this? What do I have to do to get a revision that can be installed?

toolshed • 336 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by esch004160
2
gravatar for esch0041
13 months ago by
esch004160
esch004160 wrote:

I don't see anything in the XML reference for comments saying that they cannot appear outside the root element.

Planemo serve, test, lint and shed_lint all worked fine with my tool definition XML, which ended with an XML comment that serves as a "vim modeline". Vim modelines are instructions that may be embedded in comments that give the Vim editor instructions for preferences, like what should be the tab width in spaces, should tabs be expanded to tabs etc..

My tool definition XML ended with a comment (bearing a vim modeline) that appeared after the closing <tool/> tag. Planemo. When I moved this comment before the closing <tool/> tag, the repository showed This revision can be installed: True.

ADD COMMENTlink written 13 months ago by esch004160
1

I am glad you solved this. Seems that the Tool Shed (or the library it uses for XML parsing) is more strict than the standard reference and it deemed your XML file invalid thus not allowing installation. Would you mind creating a Github Issue to start a fix for this sub-par behavior?

ADD REPLYlink written 13 months ago by Martin Čech ♦♦ 4.7k
1
gravatar for Bjoern Gruening
13 months ago by
Bjoern Gruening5.0k
Germany
Bjoern Gruening5.0k wrote:

Hi Art!

This indicates that no tool is in your repo. Next to shed_create you need to do shed_upload to really push your tool into the TS.

Hope that helps, Bjoern

ADD COMMENTlink written 13 months ago by Bjoern Gruening5.0k
1

Thanks, Bjoern.

Indeed the files are present in the repository on the testtoolshed (when I browse tip and when I hg clone), but even after shed_upload it is still marked This revision can be installed: False.

Looking at other tools, I cannot spot what I am missing in my repository.

ADD REPLYlink modified 13 months ago • written 13 months ago by esch004160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 122 users visited in the last hour