Question: How to fix FreeBayes: Conda dependency seemingly installed but failed to build job environment?
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gravatar for msprindzhuk
5 months ago by
msprindzhuk40
msprindzhuk40 wrote:

Dataset generation errors

Dataset 143: FreeBayes on data 21 and data 25 (variants) The Galaxy framework encountered the following error while attempting to run the tool:

Traceback (most recent call last): File "/home/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job job_wrapper.prepare() File "/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 "/home/galaxy/galaxy/lib/galaxy/tools/__init__.py", line 1342, in build_dependency_shell_commands tool_instance=self File "/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 "/home/galaxy/galaxy/lib/galaxy/tools/deps/resolvers/conda.py", line 249, in shell_commands self.build_environment() File "/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? thanks

freebayes • 218 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson22k • written 5 months ago by msprindzhuk40
1

Hello,

Conda may be the root of all the tool installation problems, including the SAMtool install problem here https://biostar.usegalaxy.org/p/22161/ and the VT tools problem here: https://biostar.usegalaxy.org/p/22203/

Are the dependencies resolvers set up as described here? Which option are you using? Perhaps double check the configuration and that Conda is installed correctly (does it work line-command?): https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html

Thanks, Jen, Galaxy team

ADD REPLYlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson22k
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