Biosoft=/home/viru/Biosoft
Bin=/home/viru/bin

Download java

cd ${Biosoft}
wget -O jre1.tar.gz http://javadl.oracle.com/webapps/download/AutoDL?BundleId=227542_e758a0de34e24606bca991d704f6dcbf

Uncompress java

tar zxf jre1.tar.gz
ln -s ${Biosoft}/jre1.8.0_151/bin/* ${Bin}/

Download fastqc

cd ${Biosoft}
wget -O fastqc_v0.11.5.zip http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip

Uncompress fastqc

unzip fastqc_v0.11.5.zip
cd FastQC/
chmod 755 fastqc
cd ..
ln -s ${Biosoft}/FastQC/fastqc ${Bin}/

Download trimmomatic binary_file

cd ${Biosoft}
wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
unzip Trimmomatic-0.36.zip
cd Trimmomatic-0.36/
chmod 755 trimmomatic-0.36.jar
ln -s ${Biosoft}/Trimmomatic-0.36/trimmomatic-0.36.jar ${Bin}/

Download STAR

wget wget -O star_2.5.3a.tar.gz https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz
tar -zxf star_2.5.3a.tar.gz
cd STAR-2.5.3a/
cd ${Bin}/
ln -s ../Biosoft/STAR-2.5.3a/bin/Linux_x86_64/STAR ./

Download picard

cd ${Biosoft}
wget https://github.com/broadinstitute/picard/releases/download/2.15.0/picard.jar
wget https://github.com/broadinstitute/picard/archive/2.15.0.zip
cd picard-2.15.0/
cp ../picard.jar .
cd ${Bin}
ln -s ../Biosoft/picard-2.15.0/picard.jar ./

Download GATK

wget -O GATK_3.8.tar.bz2 https://software.broadinstitute.org/gatk/download/auth?package=GATK
tar -jxf GATK_3.8.tar.bz2
cd GenomeAnalysisTK-3.8-0-ge9d806836/
chmod 755 GenomeAnalysisTK.jar
ln -s ${Biosoft}//GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar ${Bin}/

Download SAR Toolkit

wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2-1/sratoolkit.2.8.2-1-ubuntu64.tar.gz
tar -zxf sratoolkit.2.8.2-1-ubuntu64.tar.gz
cd ${Bin}
ln -s ../Biosoft/sratoolkit.2.8.2-1-ubuntu64/bin/* ./

Download SAMtools

Download zlib

wget -O zlib.tar.gz https://github.com/jtkukunas/zlib/archive/v1.2.8_jtkv4.tar.gz
tar -zxf zlib.tar.gz
cd zlib-1.2.8_jtkv4/
./configure
sudo make install

Download bzip2

wget http://bzip.org/1.0.6/bzip2-1.0.6.tar.gz
tar -zxf bzip2-1.0.6.tar.gz
cd bzip2-1.0.6/
make
sudo make install

Download liblzma

wget https://tukaani.org/xz/xz-5.2.3.tar.gz
tar -zxf xz-5.2.3.tar.gz
cd xz-5.2.3/
./configure
make
sudo make install

Download ncurses

wget ftp://ftp.gnu.org/gnu/ncurses/ncurses-6.0.tar.gz
cd ncurses-6.0/
./configure
make
sudo make install

Download htslib

wget https://github.com/samtools/samtools/releases/download/1.6/samtools-1.6.tar.bz2
tar -zxf star_2.5.3a.tar.gz