Hi Robert, The fasta file that you created the indexes from should be located in the same directory hierarchy as the indexes themselves. For some tools (Bowtie is one them), a symbolic link to the fasta file in the directory with the indexes is also required. General instructions to set up indexes: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Instructions for setting up the builds.txt and other precursor steps: http://wiki.g2.bx.psu.edu/Admin/Data%20Integration For your example, the data could be organized like: /share/shared/data/genomes/hg18/ /share/shared/data/genomes/hg18/seq /share/shared/data/genomes/hg18/seq/Homo_sapiens_assembly18.fasta /share/shared/data/genomes/hg18/bowtie/ /share/shared/data/genomes/hg18/bowtie/<bowtie_index_files> /share/shared/data/genomes/hg18/bowtie/<symbolic_link_to_fasta> -- where <symbolic_link_to_fasta> is named exactly like the original fasta file, in your case, "Homo_sapiens_assembly18.fasta" -- and where all of the <bowtie_index_files> have the full original fasta file name with the index name appended (your example has this correct) Then, in the bowtie_indices.loc file, the line will be only one row for the fasta genome, not one row for each individual index file. So, one row, tab deliminated, 4 fields: <unique_build_id> <dbkey> <display_name> <file_base_path> Where each field could be, for example: Homo_sapiens_assembly18 Hs18 Human (Homo sapiens) /share/shared/data/genomes/hg18/bowtie/Homo_sapiens_assembly18 -- note that there is no ".fasta" in the <file_base_path> field -- put all of four of these fields in one single row in the actual file, I only put them on individual lines to make the contents of each field clear -- be sure to use only tabs, no extra spaces, to deliminate the fields -- use the actual file system path in the <file_base_path> (Avoid following symbolic links, as these have been problematic in the past for some users) The sample .loc files have this information plus more examples: http://bitbucket.org/galaxy/galaxy-central/src/a10bb73f5793/tool-data/bowtie... We just started up an rsync server to host the same genomes as those available on Galaxy Main. Or, you can obtain genomes from any source - making the data available in fasta format is the only requirement. Full wiki documentation for the rsync server linked in with the other NGS setup wikis & a broader announcement will be coming out later this week, but this prior post covers the basics: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-July/010607.html Hopefully this helps you to get set up, Jen Galaxy team On 8/8/12 2:32 PM, Robert Chase wrote:

Hello,

I am trying to get the reference genomes to appear in our NGS tools. In my bowtie.loc file for instance I have the following line:

hg18 /share/shared/data/genomes/hg18/bowtie/Homo_sapiens_assembly18.fasta.1.eb wt

[galaxy@ tool-data]$ cd /share/shared/data/genomes/hg18/bowtie/ [galaxy]$ ls Homo_sapiens_assembly18.fasta.1.ebwt Homo_sapiens_assembly18.fasta.4.ebwt Homo_sapiens_assembly18.fasta.2.ebwt Homo_sapiens_assembly18.fasta.rev.1.ebwt Homo_sapiens_assembly18.fasta.3.ebwt Homo_sapiens_assembly18.fasta.rev.2.ebwt

Do the files provided in the .loc file have to be fasta files? Where can these fasta files be obtained?

-Rob

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