安装java

cd
mkdir -p biosoft/java
cd biosoft/java
wget -c -O java.tar.gz https://javadl.oracle.com/webapps/download/AutoDL?BundleId=235717_2787e4a523244c269598db4e85c51e0c &
tar -zxvf java.tar.gz
echo 'export PATH=/home/zhan/biosoft/java/jre1.8.0_191/bin:$PATH' >>~/.bashrc
source ~/.bashrc

安装fastqc

cd
mkdir -p biosoft/fastqc
cd biosoft/fastqc
wget -c -O fastqc.zip https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip
unzip fastq.zip
cd FastQC/
chmod a+x fastqc #有的软件没有课执行权限，需要加上权限
echo 'export PATH=/home/zhan/biosoft/fastqc/FastQC:$PATH ' >>~/.bashrc
source ~/.bashrc

安装trimmomatic

cd
mkdir -p biosoft/trimmomatic
cd biosoft/trimmomatic/
wget -c -O trimmotatic.zip http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
unzip trimmotatic.zip
echo 'export PATH=/home/zhan/biosoft/trimmomatic/Trimmomatic-0.38:$PATH' >>~/.bashrc
source ~/.bashrc

一般上有二进制文件，直接下载二进制文件就可以了；如果下载源代码，就还需要再编译

安装bowtie2

cd
mkdir -p biosoft/bowtie2
cd biosoft/bowtie2
wget -c https://nchc.dl.sourceforge.net/project/bowtie-bio/bowtie2/2.3.4.3/bowtie2-2.3.4.3-linux-x86_64.zip
unzip bowtie2-2.3.4.3-linux-x86_64.zip
echo 'export PATH=/home/zhan/biosoft/bowtie2/bowtie2-2.3.4.3-linux-x86_64:$PATH' >>~/.bashrc
source ~/.bashrc

安装tophat2

mkdir -p biosoft/tophat2
cd biosoft/tophat2/
wget -c https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz
tar -zxvf tophat-2.1.1.Linux_x86_64.tar.gz
echo 'export PATH=/home/zhan/biosoft/tophat2/tophat-2.1.1.Linux_x86_64:$PATH' >>~/.bashrc
source ~/.bashrc

安装cufflinks，cuffmerge，cuffquant，cuffdiff

mkdir -p biosoft/cufflinks
cd biosoft/cufflinks
wget -c http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
tar -zxvf cufflinks-2.2.1.Linux_x86_64.tar.gz
echo 'export PATH=/home/zhan/biosoft/cufflinks/cufflinks-2.2.1.Linux_x86_64:$PATH' >>~/.bashrc
source ~/.bashrc

因为安装samtools需要先安装zlib和ncurses,但是我再安装完zlib后ncurses没安装samtools就安装成了，我现在不知道会不会出错，等出错了再说吧

安装zlib

mkdir -p biosoft/zlib
cd biosoft/zlib
wget -c https://zlib.net/zlib-1.2.11.tar.gz
tar -zxvf zlib-1.2.11.tar.gz
cd zlib-1.2.11/
./configure
make install prefix=$HOME

安装samtools

mkdir -p biosoft/samtools
cd biosoft/samtools
wget -c https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar -jxvf samtools-1.9.tar.bz2
cd samtools-1.9/
./configure
make

安装biopython

mkdir -p biosoft/biopython
cd biosoft/biopython
unzip biopython-1.72.zip

安装vcftools

安装GATK

bamtools

下载igv，这个软件安装在本地就可以了，因为它是java软件，所以下载之后就可以使用了，但前提是需要先安装java

for mac

http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.15.app.zip

for windows

http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_Win_2.4.15.zip
for linux
http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.15.zip