Advanced QC module: failing in finding the tmp folder

[GoogleCodeExporter]

Hi,

I am running now the pipeline through my local client.  I ran the dvanced QC 
module overnight. It ran for 15 hours  and everything went well for the 
Interval creation step. But it stopped at the second step (realigning) and the 
error states that it cannot access to te temp directory in 
/projects1/test_pipeline/NEW_ORGANIZATION/Advanced_QC/temp/ .

the WHOLE path is owned by me, and also I can browse this folder from the 
pipeline GUI.

What do you think may be the problem?

I also attach the window with the Temp Dir parameters. As you can see as u 
suggested I de-ticked the directory source. The path is correct but seems to be 
on the local host, but to change the server address I have to tick again the 
directory source square and it gives me tons of errors. All the oaths of the 
workflows are on fgene1 and I am working on fgene1. I am running the same 
workflow on fgene3.

Fed

Original issue reported on code.google.com by federica...@gmail.com on 19 Jul 2011 at 6:00

[GoogleCodeExporter]

here the actual workflow attached. I confirm the same problem on fgene3.

cheers,

Federica

Original comment by federica...@gmail.com on 19 Jul 2011 at 11:43

Attachments:

• Advanced_QC_062711_UCI.pipe

[GoogleCodeExporter]

This is a great comment, Federica and thanks for reporting it as a bug. The 
Pipeline team looked at it, identified the problem and fixed it.

The issue is related to placing commands in shell scripts which are served for 
array jobs. However, the UCI Pipeline server uses runtime execution (no grid) 
and the command is used in Runtime.exec function.

We were able to reproduce the same problem by running the workflow locally, 
localhost but not on our servers. We created a Pipeline V.5.2.1.1 patch and I 
deployed and validated the fix on fgene1. Please test with the same workflow 
and you will see that it now works. I also asked Bernard to provision the patch 
to fix the Pipeline fgene3 server.

 - Ivo

Original comment by iwaterp...@gmail.com on 20 Jul 2011 at 10:04

[GoogleCodeExporter]

This issue is now resolved

Original comment by iwaterp...@gmail.com on 20 Jul 2011 at 10:26

• Changed state: Fixed
• Added labels: Usability