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 
directory
(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:

http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Best,
J.

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