Hello Mike,

The tutorial you were looking at was made using one of our local Galaxy instances, in advance of updating the main public server. The main server already includes most of the tools used in the examples, but two of the format conversion tools ("MasterVar to gd_snp" and "pgSnp to gd_snp") are not posted there yet.

I apologize for the delay. We are in the process of moving some of the tools from the Phenotype Association section of the toolbox to the Convert Formats section, while simultaneously migrating those and the rest of the Phenotype Association tools from their current, manually configured installation method to the new Galaxy Tool Shed paradigm. We have encountered some technical difficulties with that, but we hope to have the update accomplished within the next few weeks.

If you need it sooner, let me know and I'll send you the underlying Perl script for the "pgSnp to gd_snp" tool, so you can run that locally to convert your file and then upload the output to your Galaxy history.

Thanks for your patience!

-Cathy Riemer

---------- Forwarded message ---------- From: Sheehan, Michael - (michaelsheehan) michaelsheehan@email.arizona.edu Date: Wed, Jan 30, 2013 at 1:30 AM Subject: [galaxy-user] Converting files to gd_snp format To: "galaxy-user@lists.bx.psu.edu" galaxy-user@lists.bx.psu.edu

I would like to convert VCF files to gd_snp format to be used in some population genomic analyses. A tutorial online makes it seem like this is the correct path to follow to conduct such analyses:

http://www.bx.psu.edu/~giardine/tutorials/example2/part1/snpTable.html

I have been using Galaxy on the free public server and this tools does not appear to be present anywhere. Does anyone know where the tool has gone or is there a way to add the needed tools back?

Thanks Mike