Revision as of 10:19, 20 October 2017

Introduction

RepeatModeler has a number of dependencies. How these are installed are detailed below:

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

The same is done with RECON, which consists of the following executables:

So all these are now available in /usr/local/bin in the nodes as well.

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:

and also the following must be installed:

@@ Line 1: / Line 1: @@
-= Introdcuction =
+= 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
@@ Line 9: / Line 20: @@
 * 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