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install_cse185_deps_wks1-3.sh
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install_cse185_deps_wks1-3.sh
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#!/bin/bash
set -e
##### Week 1 ######
# Install samtools (needed to index reference fasta files)
cd /sources
wget -O samtools-1.9.tar.bz2 https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar -xjf samtools-1.9.tar.bz2
cd samtools-1.9
./configure && make && make install
# Install BWA mem
cd /sources
git clone https://github.com/lh3/bwa
cd bwa
make
cp bwa /usr/local/bin
# Install FastQC
cd /sources
wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip
unzip fastqc_v0.11.8.zip
chmod 755 FastQC/fastqc
ln -s /sources/FastQC/fastqc /usr/local/bin/fastqc
###### Week 2 ########
# Install sickle
cd /sources
git clone https://github.com/najoshi/sickle
cd sickle
make
cp sickle /usr/local/bin/sickle
# Install nxtrim
cd /sources
git clone https://github.com/sequencing/NxTrim
cd NxTrim
make
cp nxtrim /usr/local/bin/nxtrim
# Install jellyfish
cd /sources
wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.10/jellyfish-2.2.10.tar.gz
tar -xzvf jellyfish-2.2.10.tar.gz
cd jellyfish-2.2.10
./configure
make
make install
ldconfig
# Install kmer genie
cd /sources
wget http://kmergenie.bx.psu.edu/kmergenie-1.7051.tar.gz
tar -xzvf kmergenie-1.7051.tar.gz
cd kmergenie-1.7051
python3 setup.py install
# Install minia
cd /sources
git clone --recursive https://github.com/GATB/minia.git
cd minia
sh INSTALL
cp ./build/bin/minia /usr/local/bin/minia
# Install Spades
cd /sources
wget http://cab.spbu.ru/files/release3.13.0/SPAdes-3.13.0.tar.gz
tar -xzvf SPAdes-3.13.0.tar.gz
cd SPAdes-3.13.0
PREFIX=/usr/local ./spades_compile.sh
# Install bfc kmer error correction
cd /sources
git clone https://github.com/lh3/bfc
cd bfc
make
cp bfc /usr/local/bin/bfc
# Install SSPACE
cd /sources
wget https://github.com/BenLangmead/bowtie/releases/download/v1.2.2_p1/bowtie-1.2.2-linux-x86_64.zip
unzip bowtie-1.2.2-linux-x86_64.zip
cd bowtie-1.2.2-linux-x86_64
cp bowtie* /usr/local/bin/
cd /sources
git clone https://github.com/nsoranzo/sspace_basic
cd sspace_basic
cp SSPACE_Basic_v2.0.pl /usr/local/bin/SSPACE_Basic_v2.0.pl
cp -r /sources/sspace_basic/bin /usr/local/bin/
# Install Plink
cd /sources
wget http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20190304.zip
unzip plink_linux_x86_64_20190304.zip
cp plink /usr/local/bin
# Install bedtools
cd /sources
wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz
tar -zxvf bedtools-2.28.0.tar.gz
cd bedtools2
make
make install
# Install htslib (with tabix)
cd /sources
wget -O htslib-1.8.tar.bz2 https://github.com/samtools/htslib/releases/download/1.8/htslib-1.8.tar.bz2
tar -xjvf htslib-1.8.tar.bz2
cd htslib-1.8/
./configure
make
make install
# Install bcftools
cd /sources
wget -O bcftools-1.9.tar.bz2 https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2
tar -xjvf bcftools-1.9.tar.bz2
cd bcftools-1.9
./configure
make
make install
# Install VCFTools
cd /sources
wget https://github.com/vcftools/vcftools/releases/download/v0.1.16/vcftools-0.1.16.tar.gz
tar -xzvf vcftools-0.1.16.tar.gz
cd vcftools-0.1.16
./autogen.sh && ./configure && make && make install