PCA Ancestry using SNP rgEigPCA.py "$i.extra_files_path/$i.metadata.base_name" "$title" "$out_file1" "$out_file1.files_path" "$k" "$m" "$t" "$s" "$pca"

**Syntax** - **Genotype data** is the input genotype file chosen from available library files. - **Title** is used to name the output files - **Tuning parameters** documented in the Eigensoft documentation - see below (Note that you may need to convert an existing genotype file into that format to use this tool) ----- **Summary** **Attribution** This tool runs and relies on the work of many others, including the maintainers of the Eigensoft program, and the R and Bioconductor projects. For full attribution, source code and documentation, please see http://genepath.med.harvard.edu/~reich/Software.htm, http://cran.r-project.org/ and http://www.bioconductor.org/ respectively This implementation is a Galaxy tool wrapper around these third party applications. It was originally designed and written for family based data from the CAMP Illumina run of 2007 by ross lazarus (ross.lazarus@gmail.com) and incorporated into the rgenetics toolkit. copyright Ross Lazarus 2007 Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html but is about as useful as a sponge boat without EIGENSOFT pca code. **README from eigensoft2** [rerla@beast eigensoft2]$ cat README EIGENSOFT version 2.0, January 2008 (for Linux only) This is the same as our EIGENSOFT 2.0 BETA release with a few recent changes as described at http://genepath.med.harvard.edu/~reich/New_In_EIGENSOFT.htm. Features of EIGENSOFT version 2.0 include: -- Keeping track of ref/var alleles in all file formats: see CONVERTF/README -- Handling data sets up to 8 billion genotypes: see CONVERTF/README -- Output SNP weightings of each principal component: see POPGEN/README The EIGENSOFT package implements methods from the following 2 papers: Patterson N. et al. 2006 PLoS Genetics in press (population structure) Price A.L. et al. 2006 NG 38:904-9 (EIGENSTRAT stratification correction) See POPGEN/README for documentation of population structure programs. See EIGENSTRAT/README for documentation of EIGENSTRAT programs. See CONVERTF/README for documentation of programs for converting file formats. Executables and source code: ---------------------------- All C executables are in the bin/ directory. We have placed source code for all C executables in the src/ directory, for users who wish to modify and recompile our programs. For example, to recompile the eigenstrat program, type "cd src" "make eigenstrat" "mv eigenstrat ../bin" Note that some of our software will only compile if your system has the lapack package installed. (This package is used to compute eigenvectors.) Some users may need to change "blas-3" to "blas" in the Makefile, depending on how blas and lapack are installed. If cc is not available on your system, try "cp Makefile.alt Makefile" and then recompile. If you have trouble compiling and running our code, try compiling and running the pcatoy program in the src directory: "cd src" "make pcatoy" "./pcatoy" If you are unable to run the pcatoy program successfully, please contact your system administrator for help, as this is a systems issue which is beyond our scope. Your system administrator will be able to troubleshoot your systems issue using this trivial program. [You can also try running the pcatoy program in the bin directory, which we have already compiled.]