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? Yes -- [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/ lib [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. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 241 bytes Desc: not available Url : http://bioinformatics.org/pipermail/biobrew-users/attachments/20041015/0b3cac8a/attachment.bin