[BioBrew Users] Fixed modulefiles RPM or source?

Humberto Ortiz Zuazaga humberto at hpcf.upr.edu
Fri Oct 15 10:25:17 EDT 2004

glen at callident.com said:

>> The module files aren't actually being used, are they? I have none of
>> the bioinformatics tools in my path, and can't run EMBOSS programs
>> (library problems, ACD problems), because the environment isn't set up
>> for EMBOSS.

> ACD problems? 

[humberto at espresso humberto]$ showdb
-bash: showdb: command not found

[humberto at espresso humberto]$ /opt/BioBrew/EMBOSS/2.6.0/bin/showdb
/opt/BioBrew/EMBOSS/2.6.0/bin/showdb: error while loading shared libraries: 
libnucleus.so.0: cannot open shared object file: No such file or directory

[humberto at espresso humberto]$ export LD_LIBRARY_PATH=/opt/BioBrew/EMBOSS/2.6.0/

[humberto at espresso humberto]$ /opt/BioBrew/EMBOSS/2.6.0/bin/showdb

   EMBOSS An error in ajacd.c at line 1534:
acdfile '/usr/src/redhat/BUILD/EMBOSS-2.6.0/emboss/acd/showdb.acd' not opened
If you put the following statement into an .embossrc file, programs will start 
to work.

set emboss_acdroot /opt/BioBrew/EMBOSS/2.6.0/share/EMBOSS/acd

This can also be set in a sitewide emboss.default fike, but I think EMBOSS 
programs will look for it in /usr/src/redhat/BUILD/EMBOSS-2.6.0/emboss/share/EM
BOSS as well.

This may be a configure/rpmbuild problem with EMBOSS, the admin guide for 
EMBOSS says to pass an absolute path to --prefix or bad things can happen.

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