Lobstr-code

lobSTR: a short tandem repeat profiler for next generation sequencing data

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Overview

Installation from precompiled binaries

wget http://files.teamerlich.org/lobSTR/lobSTR-bin-Linux-x86_64-X.X.X.tar.gz
tar -xzf lobSTR-bin-Linux-x86_64-X.X.X.tar.gz
cd lobSTR-bin-Linux-x86_64-X.X.X
sudo cp bin/lobSTR bin/allelotype bin/lobSTRIndex /usr/local/bin
	

Installation from source

Before installing from source, make sure all required packages are installed and in the user's $PATH (see below for a list of requirements). lobSTR should compile on most Linux and Mac systems.
wget http://files.teamerlich.org/lobSTR/lobSTR-X.X.X.tar.gz
tar -xzf lobSTR-X.X.X.tar.gz
cd lobSTR-X.X.X/
./configure
make
make check
sudo make install
	  

You can find the latest version of the source code on the git repository.

Scripts will be available in $PREFIX/share/lobSTR/scripts and noise model files in $PREFIX/share/lobSTR/models. $PREFIX is by default /usr/local on Linux systems unless you specified a different prefix during the installation.

For usage instructions see usage.

Installation on Mac OSX

You can also install lobSTR using Homebrew. First make sure homebrew is installed, then run:

brew tap homebrew/science
brew install lobstr
	

Testing that lobSTR was installed correctly

To test that your lobSTR installation is working, you can run the provided test script installed to $PREFIX/share/lobSTR/scripts/lobSTR_test_run.sh. $PREFIX is by default /usr/local/. If this runs without errors, lobSTR was installed successfully.

Requirements

The packages below are required for building lobSTR from source. If you are using the precompiled binaries, these are not required.

External libraries
Program Tested on Debian/Ubuntu package Homebrew package
gcc 4.4.3 gcc gcc
g++ 4.4.3 g++ g++
automake 1.11.1 automake automake
libtool 2.2.6 libtool libtool
pkg-config 0.22 pkg-config pkg-config
boost 1.46.1 libboost-dev boost
zlib 1.2.3.3 zlib1g-dev -
cppunit 1.12.1 libcppunit-dev cppunit
gsl 1.16 libgsl10-dev gsl
Python libraries
Note: the python libraries listed below are only required for certain optional steps. All Python scripts were tested using Python 2.7.
Program Tested on Download link easy_install package lobSTR steps where required
numpy 1.8.2 download numpy Filtering VCFs
pyfasta 0.5.1 download pyfastaBuilding a custom index and building an strinfo file required for allelotyping from a custom index for v3.*.
pyvcf 0.6.7 download pyvcf Filtering VCFs, vcf-extract, vcf-to-tab
Biopython 1.5.6 download biopython Building a custom index and building an strinfo file required for allelotyping from a custom index for v2.*.