Hello Sachit,
There are a few problems with the command line. If you want to install
hg19, then hg16 should not be used. Also, the reference_in to the tool
should be an uncompressed fasta file. This is described in the tool
documentation.
You will also need to use as the 'index_basename'
How do I add hg16 into the build-in index?
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Hello Sachit,
Instructions for setting up local indexes are in our wiki here:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
Bowtie2 is not specifically listed, but the instructions for Bowtie and
Bowtie2 are nearly identical. The same indexes are used for Bowtie2 and
Tophat2. When