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Question: Tool command not found: Fatal error: Exit code 127 ()
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gravatar for sursngika
13 months ago by
sursngika • 0
sursngika • 0 wrote:

Dear All,

I installed a local instance of galaxy in a remote server. I have a workflow and installed tools required to run the workflow using tool-shed. Tools installed without error. But when I run the workflow tools give error as below. I understand its something to do with PATH. When I installed a tool e.g. Samtools in a ubuntu path, the tool works in galaxy as well. I searched this in past posts but couldn't find a clear solution to the problem. Any help would be greatly appreciated.

Error:

Fatal error: Exit code 127 () /home/vaz/sumudu/git/galaxy_infectious/galaxy-v1.0/database/jobs_directory/000/77/tool_script.sh: line 9: blastn: command not found

Thank you Rangi
admin dependency blast local • 564 views
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written 13 months ago by sursngika • 0
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gravatar for Jennifer Hillman Jackson
13 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The error does indicate that blastn is not installed or that Galaxy cannot find it.

Check to see if the tool is included in a tool suite. It may be that dependencies are not fully resolved with individual tool installs. And we would like to know which, especially if devteam or iuc owned (we can fix these - others might require contacting the tool author other ways). Example: https://biostar.usegalaxy.org/p/24044/

If that does not work, please share more details:

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson ♦ 25k
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