Repeatmodeler
Contents
Introduction
Installation notes
RepeatModeler has a number of dependencies. How these are installed are detailed below:
nseg
nseg and nmerge (included in nseg) are quite old programs coded in C by NCBI. These were installed on all machines in /usr/local/bin
RECON
The same is done with RECON, which consists of the following executables:
- imagespread
- eledef
- eleredef
- edgeredef
- famdef
So all these are now available in /usr/local/bin in the nodes as well.
RepeatScout
As this also only includes two C-coded executables with quite good names, it is easy enough to install it locally on all the nodes:
- RepeatScout
- build_lmer_table
and also the following perl scripts (using the unusual *.prl extension) must be also be installed:
- filter-stage-1.prl
- filter-stage-2.prl
- merge-lmer-tables.prl
- compare-out-to-gff.prl
RepeatModeler itself
This is quite similar to RepeatMasker, although there is an opportunity to manually edit RepModelConfig.pm.tmp which is more accurate and convenient than the automatic configure script. Predictably, it will only be active when the tmp extension is hived off.
