Problem with Trinity/Unicycler at https://usegalaxy.org -- Unicycler fixed, Trinity OPEN, follow for updates

Question: Problem with Trinity/Unicycler at https://usegalaxy.org -- Unicycler fixed, Trinity OPEN, follow for updates

4 months ago by

j_pasook • 40 wrote:

Hi,

I've tried to execute my work using Trinity (Beta) via Galaxy. Every time I execute it shows this error to me;

Can't locate Sys/Hostname.pm: Permission denied at /opt/packages/trinity/2.2.0/PerlLib/HPC/FarmIt.pm line 13. BEGIN failed--compilation aborted at /opt/packages/trinity/2.2.0/PerlLib/HPC/FarmIt.pm line 13. Compilation failed in require at /opt/packages/trinity/2.2.0/PerlLib/HPC/GridRunner.pm line 10. BEGIN failed--compilation aborted at /opt/packages/trinity/2.2.0/PerlLib/HPC/GridRunner.pm line 10. Compilation failed in require at /opt/packages/trinity/2.2.0/Trinity line 29.

I don't know it is because of my data or a server. Please help

Thanks

trinity unicycler galaxy assembly usegalaxy.org • 684 views

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modified 4 months ago by Jennifer Hillman Jackson ♦ 25k • written 4 months ago by j_pasook • 40

Hello, This might be related to some other known issues with the server at https://usegalaxy.org. Please follow this post for updates: https://biostar.usegalaxy.org/p/28860/.

I'll also run a test Trinity job to see if that cluster is also problematic - it was last week, then passed as Ok, yet other jobs that run there (Unicycler) are still erroring. It could be a distinct issue, more feedback once the tests complete.

Thanks for reporting the problem, Jen, Galaxy team

ADD REPLY • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Thanks!! I will look forward to it. Hoping that it'll get fixed soon

ADD REPLY • link written 4 months ago by j_pasook • 40

I confirmed the problem with a test run: https://github.com/galaxyproject/usegalaxy-playbook/issues/152#issuecomment-407475285

More feedback once this is fixed.

ADD REPLY • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

4 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

UPDATE 7-27-2018

Status:

Unicycler -- jobs should run correctly now (passed tests). Please let us know if you encounter a server error from a job started mid-day today or later.
Trinity -- jobs are still failing server-side, we are working on this still

Thanks! Jen, Galaxy team

ADD COMMENT • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Is there any ETA on the fix for Trinity?

ADD REPLY • link written 3 months ago by nathanshaner • 20

Do you have an idea of when the issues with Trinity might be fixed? Thank you.

ADD REPLY • link written 3 months ago by e.ransom-jones • 0

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