Indeed you need to install many many tools to make galaxy run.

You may be better off getting the cloud version, which has many tools already installed.

Getting GALAXY to run with all the tools that are provided is not a trivial task...

It gets MUCH better with the TOOLSHED option, since this can install many of the tools you may need...

the "old" way of galaxy was to rely on many of the tools to be available on the path so they magically run, but things like GATK and FASTQC etc. that are run from JAVA jars, need to be installed manually into that directory tool-data/shared/jars

Thon

On Dec 06, 2012, at 11:36 AM, greg <margeemail@gmail.com> wrote:

I'm guessing FastQC isn't installed by default?

This page give these instructions:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

FastQC (0.10.0)NGS: QC and manipulationFastQC from Babraham. The main
fastqc perl script must be executable from
tool-data/shared/jars/FastQC/fastqc

But I don't understand what it means. Do I need to download something,
change permissions? I don't have anything inside the jars folder.

Thanks,

Greg
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