Question: Tool command not found: Fatal error: Exit code 127 ()
0
gravatar for sursngika
5 months ago by
sursngika0
sursngika0 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 • 264 views
ADD COMMENTlink written 5 months ago by sursngika0
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson24k 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 COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson24k
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