venn_list ToolShed installation issue

[remimarenco]

Hi Peterjc,

I tried to install your venn_list tool from the toolshed of my Galaxy instance (v15.07) and it seems to have some troubles installing the dependency biopython / package_biopython.

If I look into the tool repository in the admin and click on venn_list, under Installed repository dependencies I can see package_biopython_1_65 is version 030f1a505d40. Whereas if I look under the Installed tool dependencies and click on biopython, then the .sh is looking for biopython/1.65/biopython/package_biopython_1_65/dc595937617c/env.sh

And there is no dc595937617c's version of package_biopython_1_65

Do you think it could be related to a misconfiguration in the tool shed or something?

Thanks!

[peterjc]

Hmm. There is some non-intuitive logic about packages and revisions when trying to satisfy dependencies. @bgruening any thoughts? Should we raise this on the galaxy-dev list?

[remimarenco]

I changed the path by hand for the env.sh by pointing to the right package and Galaxy disabled the tool (and sometimes it disappear from the tool pane):

This tool was disabled before the job completed. Please contact your Galaxy administrator.
WARNING 2015-11-04 12:13:17,644 (29632) Tool 'toolshed.g2.bx.psu.edu/repos/peterjc/venn_list/venn_list/0.0.9' removed from tool config, unable to run job galaxy.jobs.handler ERROR 2015-11-04 12:13:17,752 (29632) Error checking job readiness

[remimarenco]

Hi peter, any news on this? We would want to install your tool through the toold_shed as manual installation is a bit tricky on our server (Need an older R version)

[peterjc]

I don't know, sorry. @bgruening did the dependency work for this tool (I have only even installed the dependencies manually).

It doesn't actually care about the exact version of R, as long as limma is installed, and a matching version of rpy. You should already have a working combination of R and rpy installed for the core Galaxy tools.

My suggestion is try installing limma into that version of R manually, and then when you (re)install venn_list via the ToolShed untick the handle dependencies option.