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.
From: Peter Cock <p.j.a.cock(a)googlemail.com>
Sent: 24 May 2018 14:22:40
To: David Lee
Subject: Re: [galaxy-dev] Conda problem
On Thu, May 24, 2018 at 2:14 PM, David Lee <david.lee(a)bristol.ac.uk> wrote:
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
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
"CondaError: RuntimeError('EnforceUnusedAdapter called with url
command is using a remote connection in offline mode.\n',)"
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