Hi, Sofie - yes, that's right - third party tools are not 'bundled'
with our source distribution and must be obtained from the tool
authors and installed where they are needed - we just provide wrappers
to make them work inside Galaxy. Same goes for the large genomic data
and indexes needed by some tools such as bwa.

The Galaxy distribution includes code for some of the inbuilt tools
like the fastq groomer, but most of the distribution tool wrappers
rely on popular third party packages such as cufflinks, bwa, FastQC,
R/BioC packages and so on. There's a list of third party dependencies
at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies - they
have to be available on the computational nodes for Galaxy jobs
requiring them to run.


On Tue, Oct 4, 2011 at 10:50 AM, Sofia Robb <sofia2...@gmail.com> wrote:
> 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
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-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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