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

An error occurred running this job: Error indexing reference sequence
/bin/sh: bowtie-build: command not found
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?

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