Question: Issue "Conda dependency seemingly installed but failed to build job environment." after installing tools
gravatar for TWV
8 months ago by
TWV20 wrote:

I just installed some tools on a local galaxy instance, and soon after I received the error "Conda dependency seemingly installed but failed to build job environment." for any job I tried to run, regardless of uploading files, or using a simple tool from the toolshed. Restarting galaxy or removing the tools did not help.

The tools were " samtools_stats" by devteam, " samtools_idxstats" by devteam and "rmarkdown_samtools_flagstat" by mingchen0919.

The galaxy version is 17.09.

when I type "which conda" in bash I get no output.

Upon launching galaxy, there is a wall of text for each package saying

Requirement already satisfied:.....

Furthermore, the last message is DEBUG 2018-03-22 15:28:03,620 Unable to find config file './dependency_resolvers_conf.xml'

EDIT: I checked some logs and turns out these messages have always been there, while the problem is recent. so it is likely unrelated.

Help is much appreciated!

EDIT2: Since I am not an informatician, and troubleshooting the issue myself would have taken too much time, I decided to update the server to version 18.01, and it solved the issue.

Ende gut, alles gut.

Greetings, Wolf.

tool dependency conda • 529 views
ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson25k • written 8 months ago by TWV20
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Glad upgrading Galaxy to 18.01 worked. How dependencies install has changed considerably over the last year and tools are designed to now work with the new methods.

For others running an older Galaxy version, that may run into problems, these are the release notes detailing out the changes:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 8 months ago by Jennifer Hillman Jackson25k
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