SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Running Pindel prior to Dindel jtjli Bioinformatics 32 03-17-2012 01:53 PM
can I automate running dindel? libiyagirl Bioinformatics 5 03-04-2011 11:27 AM
problem running Dindel on MacOSX 10.6.4 csoong Bioinformatics 5 12-23-2010 07:12 AM
xgrid with Mac OSx feng Bioinformatics 0 11-28-2010 07:55 AM
Xgrid Jerry Glenn Bioinformatics 0 10-29-2010 09:34 AM

Reply
 
Thread Tools
Old 05-19-2011, 02:30 AM   #1
olivier
Junior Member
 
Location: Paris

Join Date: May 2011
Posts: 3
Default Running Dindel on OS X with XGRID

Hi,

I had successfully installed dindel on 5 OSX 10.6.4 computer and server. Exactly the same install for all, with exactly the same paths for all.

Dindel was successfully compiled with the same modified Makefile (add boost library file, path to samtools dir, remove static flag) and run locally on each computer but if I want to submit a dindel job trough the xgrid command :

xserver$ xgrid -job submit /opt/local/bin/dindel {
jobIdentifier = 50;
}
xserver$ xgrid -job results -id 50
dyld: Library not loaded: /opt/local/lib/libboost_program_options.dylib
Referenced from: /opt/local/bin/dindel
Reason: no suitable image found. Did find:
/opt/local/lib/libboost_program_options.dylib: open() failed with errno=1


if i look in /usr/include/sys/errno.h for what is errno number 1 I had a very useful : #define EPERM 1 /* Operation not permitted */

Did someone have had the same problem and find a fix for it ?

Thank's
olivier is offline   Reply With Quote
Old 05-19-2011, 07:31 AM   #2
olivier
Junior Member
 
Location: Paris

Join Date: May 2011
Posts: 3
Default solution

I reply to myself as I solved my problem, but it may be usefull for others.

Actually the problem was due to the sandbox access use by xgrid.

You could find explanations here :

http://lists.apple.com/faq/pub/xgrid...&id=26&lang=en

in brief it is a permision problem. if you don't use kerberos run on xgrid will go as nobody and it don't have enought rigth to write. the good practice is to use kerberos.

The quick and dirty way is this one (on each xgrid agent) but IT'S A SECURITY HOLE!

$ sudo mv /usr/share/sandbox/xgridagentd_task_nobody{,.orig}.sb

$ sudo cp /usr/share/sandbox/xgridagentd_task_{some,no}body.sb

--Olivier
olivier is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:08 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO