Conda problem

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Conda problem

David Lee

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. 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."


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?


Regards, David


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Re: Conda problem

Peter Cock
On Thu, May 24, 2018 at 2:14 PM, David Lee <[hidden email]> 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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Re: Conda problem

David Lee

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 <[hidden email]>
Sent: 24 May 2018 14:22:40
To: David Lee
Cc: [hidden email]
Subject: Re: [galaxy-dev] Conda problem
 
On Thu, May 24, 2018 at 2:14 PM, David Lee <[hidden email]> 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
> <a href="https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2018.4.16-0.tar.bz2\nThis"> 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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Re: Conda problem

Peter Cock
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 <[hidden email]> 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 <[hidden email]>
> Sent: 24 May 2018 14:22:40
> To: David Lee
> Cc: [hidden email]
> Subject: Re: [galaxy-dev] Conda problem
>
> On Thu, May 24, 2018 at 2:14 PM, David Lee <[hidden email]> 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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and other Galaxy lists, please use the interface at:
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