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
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
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
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.lee@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.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
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Peter Cock