I have installed the local galaxy distribution on my MacBook Pro Mac OS X Version 10.7.1 using hg as described on get galaxy.org

         hg clone https://bitbucket.org/galaxy/galaxy-dist/

the run.sh script runs, and i am able to open localhost:8080 and i am able to upload data files.

I have not tested many applications but it seems that the applications are not installed, or at least bwa and bowtie are not installed from the error I receive. 

An error occurred running this job: Error indexing reference sequence

/bin/sh: bowtie-build: command not found

-and-

An error occurred running this job: Could not determine BWA version

Error indexing reference sequence. /bin/sh: bwa: command not found

Are the applications not installed?  I searched for them but could not find them within /galaxy-dist (find /galaxy-dist -name "*bwa*" ). I find wrappers but no apps. Where should they be located?

Thanks,

Sofia