Question: Problem with dependencies: Conda/freebayes
gravatar for Mesohexaploid
15 days ago by
Mesohexaploid 10 wrote:

Dear Galaxy Team,

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

Galaxy correctly installed freebayes (, 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.


conda tool shed freebayes • 129 views
ADD COMMENTlink written 15 days ago by Mesohexaploid 10

Have you tried just reinstalling it?

ADD REPLYlink written 14 days ago by Devon Ryan1.9k

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

ADD REPLYlink written 14 days ago by Mesohexaploid 10
gravatar for Devon Ryan
10 days ago by
Devon Ryan1.9k
Devon Ryan1.9k wrote:

Can you manually create the __parallel@20170422 conda environment (it should have parallel-20170422 and perl- 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 COMMENTlink modified 10 days ago • written 10 days ago by Devon Ryan1.9k

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.


ADD REPLYlink written 7 days ago by Mesohexaploid 10
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