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01 Installation

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Sebastian Beier edited this page Mar 11, 2019 · 9 revisions

Installation

This instructions will help you to install kmasker including all prerequisites.

Prerequisites

To install and use kmasker you will need several tools and libraries on your system:

  • git
  • blast
  • jellyfish >= 2.2.6
  • libjellyfish-devel
  • libpthread (most likely already installed)
  • fastq-stats from ea-utils
  • libgsl(-devel)
  • gffread
  • GCLIB as part of gffreads install instructions
  • perl5
  • python (>=3.5) including pandas & numpy
  • scons
  • tools for compiling c++ programs (we will try to offer binaries for differet OS to you)

Installation Instructions

Distribution specific parts

Ubuntu/Debian

Installation of necessary tools and libs with apt

apt-get install jellyfish libjellyfish-2.0-dev gsl libgsl-dev scons blast2 build-essential

Redhat/CentOS

Installation of necessary tools and libs with yum To be done.

General instructions (executed after the distrubution dependencies)

Create a directory for the source code of the different tools mkdir ~/src Check out the tools

cd ~/src
git clone https://github.com/ExpressionAnalysis/ea-utils
git clone https://github.com/gpertea/gclib
git clone https://github.com/gpertea/gffread
git clone https://github.com/tschmutzer/kmasker
cd ea-utils/clipper
make fastq-stats

#Copy the binary file to a location which is in your path
#or to KMASKERs bin directory
cd ../..
cd gffread
make
cd ..

#Compile cmasker using scons. First, change into 'scr' directory
cd kmasker/src
# Make sure path libraries are set correct. To do so you can use the listed 
# 'export' commands. 
# Please modify path corresponding to your installations.
# export LD_LIBRARY_PATH=/path/to/jellyfish/2.2.6/lib/:$LD_LIBRARY_PATH
# export CPATH=/path/to/jellyfish/jellyfish/2.2.6/include/jellyfish-2.2.6/:$CPATH
# export LIBRARY_PATH=/path/to/jellyfish/2.2.6/lib/:$LIBRARY_PATH
scons
cp cmasker ../bin
cd ..

cp ../ea-utils/clipper/fastq-stats bin/
cp ../gffread/gffread bin/
#if you want you can add KMASKERs bin directory
#to your path
export PATH=$PATH:/$HOME/src/kmasker/bin

MacOS

On MacOS the instructions are slightly different. To be done.

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