Hi Julie, 

any chance you are setting PYTHONPATH before starting galaxy's job handlers (a common place would the supervisor config, in case you're using that)?

This will interfere with all python modules that are installed via conda.

Best,

Marius

On 3 October 2017 at 09:13, julie dubois <dubjulie@gmail.com> wrote:

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
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/
>
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/