Hi Peter,


Thanks for your reply which nudged me in the right direction and the problem seems to be solved. Although I uninstalled samtools and samba from Galaxy there were remnants of the packages remaining in galaxy/database/dependencies/_conda/envs and galaxy/database/dependencies/_conda/pkgs/. After I deleted these directories the error messages disappeared and tools are running again.


Cheers, David

From: Peter Cock <p.j.a.cock@googlemail.com>
Sent: 24 May 2018 14:22:40
To: David Lee
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Conda problem
 
On Thu, May 24, 2018 at 2:14 PM, David Lee <david.lee@bristol.ac.uk> wrote:
> Hi,
>
>
> I hope somebody can help me with this. I've been maintaining a Galaxy
> installation for the past few months that has suddenly developed a problem
> that I can't undo.

Which version of Galaxy? Can you tell what version of conda it is using?

> I think it occurred after installing samtools and sambamba packages
> which I have subsequently uninstalled but which has made no
> difference. Every tool I try to run fails with this error:
>
> "Conda dependency failed to build job environment. This is most likely
> a limitation in conda. You can try to shorten the path to the
> job_working_directory."
>

There are some very long path names used in Conda, perhaps
something has pushed you over an OS limit (like the longest
allowed command line)?

>
> Also, in the paster.log file I'm seeing this error that I've never seen
> before:
>
>
> "CondaError: RuntimeError('EnforceUnusedAdapter called with url
> https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2018.4.16-0.tar.bz2\nThis
> command is using a remote connection in offline mode.\n',)"
>
>
> Any suggestions?

This could be a different issue with similar symptoms, but there
is a known issue in conda 4.3.17, fixed in conda 4.4.0, which looks
related: https://github.com/conda/conda/issues/5443

Peter