Running RepeatMasker

Wanted to run RepeatMasker on the Geoduck genome to look for transposable elements, but realized that my old install of RepeatMasker went away when Emu’s hard drive crashed on like the second day of it’s existence (The joys of installing Linux on Macs) so I had to reinstall it.

Following my directions from here got me most of the way, but there were a few issues.

First, the perl module Text::Soundex installed with CPAN (Perl module manager) wasn’t installing in the right version of perl (Linux has a base install of perl, and you can have a personal install of perl, they weren’t jivving nicely) and Perl isn’t nice to allow you to change @INC locations after compilation. I cheated my way past this by copying the Soundex.pm to a directory in the @INC location, and that made it happy.

Secondly, GIRI apparently changed their Repeat Masker Library names recently, but not RepeatMasker itself, so I had to go fishing for an older version of the libraries to make RepeatMasker happy. The ones I found are here.

After all that, I have RepeatMasker running. Yay.

Advertisements