Difference between revisions of "Repeatmodeler"

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= Introdcuction =
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= Introduction =
  
It consists of the following executables:
+
 
 +
= 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
 
* imagespread
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* famdef
 
* famdef
  
= Installation notes =
+
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
  
'''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'''
+
and also the following must be installed:
  
Similarly RECON
+
* filter-stage-1.prl
 +
* filter-stage-2.prl
 +
* merge-lmer-tables.prl
 +
* compare-out-to-gff.prl

Revision as of 10:19, 20 October 2017

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 must be installed:

  • filter-stage-1.prl
  • filter-stage-2.prl
  • merge-lmer-tables.prl
  • compare-out-to-gff.prl