Installations

#go to home directory
cdh

#make a directory to put all our scripts for the course in
mkdir radBin
cd radBin


#add the path to this directory to your path variable
cdh
nano .bash_profile
#paste the following:
export PATH="$PATH:~/radBin"

#then source the .bash_profile
cdh
source .bash_profile

#create a test script and make it executable
cd ~/radBin
echo '#!/bin/bash
echo SUCCESS' > binPathTest.sh
chmod u+x binPathTest.sh


#now go to $SCRATCH and see if you can execute it
cds
binPathTest.sh


#if returns SUCCESS, then it's working
#now we have a bin to put all our RAD scripts in.

#navigate to home
cdh


#copy the repositories from github
git clone https://github.com/z0on/2bRAD_denovo.git
git clone https://github.com/z0on/2bRAD_GATK.git


#copy the scripts from each to the bin
cp 2bRAD_denovo/* radBin/
cp 2bRAD_GATK/* radBin/


#make sure they are executable
cd ~/radBin
chmod +x *.pl 
chmod +x *.py
chmod +x *.R


#test it worked
cds
uniq2loci.pl -h


#if you get a help menu it worked

#go to home directory
cdh

#clone vcftools from gitub
git clone https://github.com/vcftools/vcftools.git

#install locally by configuring with --prefix set to the vcftools directory
cd vcftools
./autogen.sh 
./configure --prefix=$HOME/vcftools
make
make install

#now navigate to where the executables were installed
cd bin

#copy these to our radBin
cp vcf* ~/radBin

#test it worked
cds
vcftools -h


#if you get the version number back it worked

#go to home dir
cdh


#get cdhit from github
git clone https://github.com/weizhongli/cdhit.git


#make installation
cd cdhit/
make

#copy the executables over to our radBin
cp cd* ~/radBin


#test
cds
cd-hit-est -h


#if you get help menus it worked

#go to home dir
cdh


#download and decompress plink
wget http://s3.amazonaws.com/plink2-assets/plink2_linux_avx2_20191126.zip
unzip plink2_linux_avx2_20191126.zip


#move to radBin
mv plink2 ~/radBin


#test
cds
plink2 -h

#go to home dir
cdh


#download admixture and decompress
wget http://software.genetics.ucla.edu/admixture/binaries/admixture_linux-1.3.0.tar.gz
tar -zxvf admixture_linux-1.3.0.tar.gz


#copy the executable to radBin
cp admixture_linux-1.3.0/admixture ~/radBin/


#test
cds
admixture

#navidate to home
cdh


#get twisst
git clone https://github.com/simonhmartin/twisst.git

#install cutadapt
cdh
pip install --user cutadapt


#copy the executable to bin
cp .local/bin/cutadapt ~/radBin/


#test
cds
cutadapt -h

#install with pip
cdh
pip install --user VCF-kit
cp .local/bin/vk ~/radBin/


#test
cds
module load bwa
module load samtools
module load blast
vk -h

#(This one is an older version, but easier to install)
#download from here:
https://sourceforge.net/projects/vcftools/files/

#navigate to directory and make
cd vcftools_0.1.13
make

#add the bin to your path for easy access
eg:
export PATH="$PATH:/Applications/vcftools_0.1.13/bin"