relshire/epigbs

Code for working with epiGBS data

epiGBS

Code for working with epiGBS data.

Install requirements

1.Tools and dependencies

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install build-essential git zlib1g zlib1g-dev lbzip2 \
bzip2 dh-autoreconf python-pip python-dev pigz ncurses-dev \
libpng-dev libfreetype6-dev pkg-config gfortran \
libopenblas-dev liblapack-dev

2.PEAR: a fast and accurate Illumina Paired-End reAd mergeR

wget http://sco.h-its.org/exelixis/web/software/pear/files/pear-0.9.10-bin-64.tar.gz
tar -xf pear-0.9.10-bin-64.tar.gz
sudo cp pear-0.9.10-bin-64/pear-0.9.10-bin-64 /usr/local/bin
sudo ln -s /usr/local/bin/pear-0.9.10-bin-64 /usr/local/bin/pear

3.vsearch

git clone https://github.com/torognes/vsearch.git
cd vsearch
./autogen.sh
./configure
make
sudo make install
cd

4.Seqtk

git clone https://github.com/lh3/seqtk.git
cd seqtk
make
sudo cp seqtk /usr/local/bin/
cd

5.samtools

wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
tar -xf samtools-1.3.1.tar.bz2
cd samtools-1.3.1
./configure
make
sudo make install
cd

6.bcftools

wget https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2
tar -xf bcftools-1.3.1.tar.bz2
cd bcftools-1.3.1
make
sudo make install
cd

7.bwa-mem

git clone https://github.com/lh3/bwa.git
cd bwa
make
find ./ -maxdepth 1 -type f -perm /a+x -exec sudo cp {} /usr/local/bin \;
cd

8.seqtk

git clone https://github.com/lh3/seqtk)
cd seqtk
make
sudo cp seqtk /usr/local/bin/

9.sambamba follow instructions on website.

git clone https://github.com/lomereiter/sambamba
cd sambamba
make

10. Install remaining requirements with pip

```SH
git clone https://github.com/thomasvangurp/epiGBS
sudo pip install -r epiGBS/requirements.txt

10. usearch (C) Copyright 2013 Robert C. Edgar, all rights reserved.

Click here and follow the instructions to get the 32bit binary.

sudo cp /path/to/usearch9.2.64_i86linux32 /usr/local/bin/
sudo cp usearch9.2.64_i86linux32 /usr/local/bin/
sudo chmod +x /usr/local/bin/usearch9.2.64_i86linux32
sudo ln -s /usr/local/bin/usearch9.2.64_i86linux32 /usr/local/bin/usearch