There's something still broken with modules on the BioBrew 3.3 roll. $ module avail --------------------------- /opt/BioBrew/modulefiles --------------------------- ClustalW/1.8.3-1 HMMER/2.3.2-pvm gromacs/3.2.1-1 Fasta/3.4-1 NCBI/6.1.0-2 wise/2.2.0-1 $ module add NCBI/6.1.0-2 $ module list Currently Loaded Modulefiles: 1) NCBI/6.1.0-2 $ blast -bash: blast: command not found $ echo $PATH /opt/BioBrew/NCBI/6.1.0-2/bin:/opt/gridengine/bin/glinux:/opt/BioBrew/mrbayes/3 .0/bin:/usr/kerberos/bin:/opt/FarmTools/fbsng/bin:/usr/local/bin:/bin:/usr/bin: /usr/X11R6/bin:/opt/ganglia/bin:/usr/java/j2sdk1.4.2_04/bin:/opt/rocks/bin:/opt /rocks/sbin:/home/humberto/bin But the actual location of blast is /opt/BioBrew/NCBI/6.1.0/bin/blast So the module is incorrectly adding the rpm version number into the path.