Installations
- Groves B Dixon
Owned by
On TACC:
Make a bin for class Expand source
#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 $SCRATCH and see if you can execute it cds binPathTest.sh #if returns SUCCESS, then it's working #now we have a bin to put all our RAD scripts in.
Get 2bRAD scripts Expand source
#navigate to home cdh #copy the repositories from github git clone https://github.com/z0on/2bRAD_denovo.git git clone https://github.com/z0on/2bRAD_GATK.git #copy the scripts from each to the bin cp 2bRAD_denovo/* radBin/ cp 2bRAD_GATK/* radBin/ #make sure they are executable cd ~/radBin chmod +x *.pl chmod +x *.py chmod +x *.R #test it worked cds uniq2loci.pl -h #if you get a help menu it worked
Install VCFtools Expand source
#go to home directory cdh #clone vcftools from gitub git clone https://github.com/vcftools/vcftools.git #install locally by configuring with --prefix set to the vcftools directory cd vcftools ./autogen.sh ./configure --prefix=$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
Install cdhit Expand source
#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
Install Plink Expand source
#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
Install Admixture Expand source
#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
Install Twisst Expand source
#navidate to home cdh #get twisst git clone https://github.com/simonhmartin/twisst.git
Install cutadapt Expand source
#install cutadapt cdh pip install --user cutadapt #copy the executable to bin cp .local/bin/cutadapt ~/radBin/ #test cds cutadapt -h
Install VCF-kit Expand source
#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
On personal computer (optional):
Install VCFtools Expand source
#(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"