Question: How to set up Prokka on Galaxy instance correctly?
0
gravatar for msprindzhuk
13 months ago by
msprindzhuk50
msprindzhuk50 wrote:

On running Prokka we have:

The Galaxy framework encountered the following error while attempting to run the tool:

Traceback (most recent call last): File "/media/home/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job job_wrapper.prepare() File "/media/home/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 913, in prepare self.dependency_shell_commands = self.tool.build_dependency_shell_commands(job_directory=self.working_directory) File "/media/home/galaxy/galaxy/lib/galaxy/tools/__init__.py", line 1342, in build_dependency_shell_commands tool_instance=self File "/media/home/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py", line 104, in dependency_shell_commands return [dependency.shell_commands(requirement) for requirement, dependency in requirement_to_dependency.items()] File "/media/home/galaxy/galaxy/lib/galaxy/tools/deps/resolvers/conda.py", line 249, in shell_commands self.build_environment() File "/media/home/galaxy/galaxy/lib/galaxy/tools/deps/resolvers/conda.py", line 244, in build_environment raise DependencyException("Conda dependency seemingly installed but failed to build job environment.") DependencyException: Conda dependency seemingly installed but failed to build job environment.

Tool execution generated the following error message:

Conda dependency seemingly installed but failed to build job environment.

How to fix that?

prokka • 359 views
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson25k • written 13 months ago by msprindzhuk50
0
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Did you try fixing it the same way you did for Freebayes (https://biostar.usegalaxy.org/p/22159/)? Using Conda and managed dependencies? It seems like however your resolvers are set up are not accessing conda correctly.

https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson25k
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