Problem with dependencies: Conda/freebayes

Question: Problem with dependencies: Conda/freebayes

10 months ago by

Dear Galaxy Team,

We encountered a problem while installing freebayes and its dependencies via Tool Shed.

Galaxy correctly installed freebayes (1.1.0.46), samtools (0.1.19) and gawk (4.1.3) (all have the Current Installation Status "Installed through Conda"), but then failed on the last dependency "parallel" (Status: "Not Installed").

The strange thing is: parallel was installed correctly. Its callable from the command line, (e.g. parallel --help works fine) and installed with the latest version. But it's not recognized by Galaxy.

We are using the Galaxy - Docker image in Version 17.09.

We would greatly appreciate any advice on how to resolve this issue.

Regards

conda tool shed freebayes • 535 views

ADD COMMENT • link •

written 10 months ago by Mesohexaploid • 10

Have you tried just reinstalling it?

ADD REPLY • link written 10 months ago by Devon Ryan • 1.9k

Yes, the tools, parallel, and our entire Galaxy instance. The issues remained...

ADD REPLY • link written 10 months ago by Mesohexaploid • 10

10 months ago by

Devon Ryan • 1.9k

Germany

Devon Ryan • 1.9k wrote:

Can you manually create the __parallel@20170422 conda environment (it should have parallel-20170422 and perl-5.22.0.1)? I'm also running 17.09 and this all installed OK on my instance via conda. What may be happening is that conda is having trouble resolving a dependency for some odd reason (this happens on occasion, you can just create the env manually and then install all of the stuff yourself).

ADD COMMENT • link modified 10 months ago • written 10 months ago by Devon Ryan • 1.9k

Hello Devon,

Thank you for your response. It appears to be that the dependency issue was somehow resolved after the n-th attempt at re-installation.

Regards

ADD REPLY • link written 10 months ago by Mesohexaploid • 10

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