Running Eigenstrat?

Question

[Darren J. Fitzpatrick]

Hi,

I am trying to run Eigenstrat on a set of ~400,000 SNPs.

The software suite provides a wrapper perl script (smartpca.perl) which takes command line arguments, formats a parameter file and calls smartpca.

When the program reaches the point of calling smartpca, I get an error saying 'Cannot execute binary'. I am running Fedora 13. Are there extra packages, compilers, etc. that I may require in order to execute smartpca?

Thanks, D.

Answer 1

[Darren J. Fitzpatrick]

I posted the solution to my qualm in my blog.

Hopefully it may be helpful to others.

D.

[biohack92]

@Darren, the link seems to not be working. Care to share the results?

Answer 2

[Pierre Lindenbaum]

from the source code: http://genetsim.org/class/EIG3.0/bin/smartpca.perl I can see that this script call several external programs (ploteig, evec2pca.perl, smartpca) using a command system(...) .

Please check that those binaries are located in the $PATH variable.

[Darren J. Fitzpatrick]

Yep - the path is correct. I believe I have solved it and will post the details of my installation when I am absolutely certain. D.

[biohack92]

@Darren Care to share the results of your troubleshooting?