Because your questions are about a local installation of Galaxy, your email is
best suited to the galaxy-dev mailing list, so I've moved it there.
> 1. FastQC not running . gives an error and doesn’t run on groomed or
> un-groomed FastQ file. The error message shows in the below pic.
I don't see the pic, you probably need to install FastQC:
(a) download the tool
(b) put the fastqc script in the <galaxy_home>/tool-data/shared/jars/FastQC
(c) make the script executable:
%chmod 777 <galaxy_home>/tool-data/shared/jars/FastQC/fastqc
> 2. No reference genomein the drop down list in TOPHAT for illumine tool
> and TOPHAt2.
See the section 'Setting Up the Reference Genomes for NGS Tools' on this page
for help setting up genomes/indices:
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