Thanks Thon. What is the TOOLSHED option?
As far as FASTQC, I downloaded and extracted it, but now what? Do I
dump all of those files and directories in tool-data/shared/jars?
> unzip fastqc_v0.10.1.zip
> ls FastQC/
Contaminants fastqc fastqc_icon.ico Help INSTALL.txt
jbzip2-0.9.jar LICENSE.txt README.txt RELEASE_NOTES.txt
run_fastqc.bat sam-1.32.jar Templates uk
On Thu, Dec 6, 2012 at 6:40 PM, Anthonius deBoer <thondeb...@me.com> wrote:
> Hi Greg,
> 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
> 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
> On Dec 06, 2012, at 11:36 AM, greg <margeem...@gmail.com> wrote:
> I'm guessing FastQC isn't installed by default?
> This page give these instructions:
> FastQC (0.10.0)NGS: QC and manipulationFastQC from Babraham. The main
> fastqc perl script must be executable from
> 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.
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