I'm a very new to a local installation of Galaxy. I have insyalled a local copy by:
% git clone https://github.com/galaxyproject/galaxy/
Is the Galaxy Shed the main official source I have to get the main tools - bowtie, tophat, cufflinks, samtools etc? (I suppose they did not came with the copy? And how to be sure that I put all the basic ones as the web-version so all my analysis tabs are working properly?)
More over what is the case of the reference genomes - is there a Galaxy Shed for genomes and such?