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? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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