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kbradnam/repeatmasker_install_instructions.md

Last active May 4, 2016 08:08
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Instructions for installing RepeatMasker on a server with Repbase database and RMBlast
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repeatmasker_install_instructions.md

Installing RepeatMasker on Mac OS X

Before we can install RepeatMasker itself, we need to install RMBlast, TRF (already installed on our server), and the repeat database Repbase. RepeatMasker also requires Perl 5.8.0 or higher.

RMBlast

RMBlast utilizes NCBI BLAST+ but you have to download a separate BLAST binary from NCBI. See the RMBlast page at RepeatMasker's website for details.

cd /Korflab/Packages
mkdir RMBlast
cd RMBlast
curl -O ftp://ftp.ncbi.nlm.nih.gov//blast/executables/rmblast/LATEST/ncbi-rmblastn-2.2.28-universal-macosx.tar.gz
tar -xvzf ncbi-rmblastn-2.2.28-universal-macosx.tar.gz
ln -s ncbi-rmblast-2.2.28 current
cd /Korflab/bin
ln -s ../Packages/RMBlast/current/bin/rmblastn

Repbase

Need to use account to download the RepeatMasker version of RepBase from the Repbase site.

cd /Korflab/Packages
mkdir Repbase
cd Repbase

Download the latest version through the RepBase (authentication required).

mv ~/Downloads/repeatmaskerlibraries-20140131.tar.gz .
tar -xvzf repeatmaskerlibraries-20140131.tar.gz
ln -s Libraries/ current

RepeatMasker

Can now proceed with RepeatMasker installation:

cd /Korflab/Packages
mkdir RepeatMasker
cd RepeatMasker
curl -O http://repeatmasker.org/RepeatMasker-open-4-0-5.tar.gz
tar -xvzf RepeatMasker-open-4-0-5.tar.gz 6.
mv RepeatMasker RepeatMasker_4.0.5
ln -s RepeatMasker_4.0.5 current
cd RepeatMasker_4.0.5/Libraries
mv RepeatMaskerLib.embl RepeatMaskerLib.embl.bak # else next step will overwrite?
ln -s ../../../Repbase/current/RepeatMaskerLib.embl
cd /Korflab/Packages/RepeatMasker/RepeatMasker_4.0.5

The configure script seems to require you to be inside the full version of the RepeatMasker directory (e.g. /Volumes/Data/Korflab/Packages etc.). This may have implications for running RepeatMasker from other machines trying to access the shared Korflab directory (which is only ever mounted at /Korflab).

So I edited the onfigure script to remove the initical directory check. Then resume as normal:

perl ./configure

Answer questions: I used 'env' for the Perl environment, and /Korflab/bin for RMBlast and trf install paths, and /Korflab/Packages/RepeatMasker/current for RepeatMasker install directory.

cd /Korflab/bin
ln -s ../Packages/RepeatMasker/current/RepeatMasker
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