Good thinking, and that's useful advice if something like this comes up again.
I wonder if there is a bug here somewhere (remnants of the environment
remaining)?
Peter
On Thu, May 24, 2018 at 4:28 PM, David Lee <david....@bristol.ac.uk> wrote:
> 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.c...@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....@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
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