Version: 3.0.3
Modulefile: software/bioinf/pyRAD/3.0.3
Prerequisites: Python/2.7.7,
software/bioinf/vsearch / software/bioinf/usearch,
software/bioinf/muscle,
(software/bioinf/PEAR)

You don't really need to load the modulefiles for the other bioinf packages if you specify the full path to them in lines 4 and 5 in params.txt:

params.txt
[...]
/cluster/Apps/bioinf/vsearch/1.1.1/vsearch    ## 4. command (or path) to call vsearch (or usearch)    (s3,s6)
/cluster/Apps/bioinf/muscle/3.8.31_i86/muscle ## 5. command (or path) to call muscle                  (s3,s7)
[...]