Dear Greg,
I read your discussion with @bgruening and I think it's not exactly
the same. Because in my case, The executable IS present in my
galaxy-dist/tool_dependency/_conda/envs/__deeptools@2.5.1/bin .
The problem is far away in the execution when the tool (computeMatrix
in my example) try to load the python module deeptools.computeMatrix.
So is there a solution to discover where is the problem ?

Thanks

2017-10-02 15:16 GMT+02:00 Von Kuster, Greg <ghv2@psu.edu>:
> This looks like the issue I’ve recently seen as well - I just discussed this
> with @bgruening on gitter - https://gitter.im/galaxy-iuc/iuc.  I’m using a
> work-around of creating the __deeptools conda env manually.  In my case, I’m
> not installing the whole suite, just the bamCoverage tool from the TS -
> https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/5d11599b8a7d.
> My work-around is to create the conda env manually:
>
> $conda create -n __deeptools@2.5.1 deep tools=2.5.1
>
> This env is created in the conda environment outside of Galaxy, so I just
> copy it to the conda environment I’ve configured for Galaxy.  This works,
> but it seems there is some issue with the installation from the TS, so
> perhaps a more ling term fix is needed.
>
>
> On Oct 2, 2017, at 8:59 AM, julie dubois <dubjulie@gmail.com> wrote:
>
> Hi dev team,
>
> I have a very big problem since I updated to galaxy 17.05 with
> deeptools from toolshed.
>
> Due to a bug in galaxy 17.05 with toolshed installed tools (reported
> in this issue https://github.com/galaxyproject/galaxy/issues/4591), I
> re-installed deeptools to try to resolve it.
> Not resolved really but it's another problem. I temporarly bypassed it.
>
> Here is my problem : I've installed deeptools from toolshed and when
> we try to use "compute matrix" for example, we have this error message
> :
>
> Fatal error: Exit code 1 ()
> Traceback (most recent call last):
>  File "/usr/local/bin/computeMatrix", line 4, in <module>
>    from deeptools.computeMatrix import main
> ImportError: No module named deeptools.computeMatrix
>
> It seems that wrapper are installed but not the tool "deeptools".
>
> For more information, here it's the way for the installation :
> search and install via toolshed
> Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a)
> Info in Manage tool dependencies : version=2.5.1, resolver=Conda,
> green check symbol in the line with a list of all deeptools.
>
> Galaxy 17.05, commit cfabe37 (21 sept 2017)
>
> I've tried to uninstall/reinstall dependencies with conda but without
> success.
>
> Have you any idea to install the deeptools please ?
>
> Thanks.
> Julie
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