Re: [galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?

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 to the tool should be an uncompressed fasta file. This is described in the tool documentation. You will also need to use as the '' the same dbkey identifier fo

Re: [galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?

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 bu