linux 安装SAMtools，bcftools，htslib，sratoolkit，bedtools,GATK，TrimGalore，qualimap，vcftools，bwa

--------------------安装Samtools-----------------------------------------------------------------------------------

1) 下载 http://www.htslib.org/download/

2) tar -jxvf samtools-1.9.tar.bz2

3）cd samtools-1.9

4）make

5) make prefix=/home/jxdong/biosoft/samtools-1.9 install

6)添加环境变量echo ' erport PATH=/home/jxdong/biosoft/samtools-1.9/bin:$PATH' >> ~/.bashrc

7)source  ~/.bashrc

----------------------安装bcftools-------------------------------------------------------------------------------

1）下载http://www.htslib.org/download/

2）tar jxvf samtools-1.9.tar.bz2

3）cd bcftools-1.9/

4）make

5）make prefix=/home/jxdong/biosoft/bcftools-1.9  install

6）添加环境变量 echo 'export PATH=/home/jxdong/biosoft/bcftools-1.9/bin:$PATH' >>~/.bashrc

7)source ~/.bashrc

----------------------安装htslib----------------------------------------------------------------------------------

1)下载http://www.htslib.org/download/

2）tar jxvf htslib-1.9.tar.bz2

3) cd htslib-1.9/

4）make

5) make prefix=/home/jxdong/biosoft/htslib-1.9 install

6)添加环境变量 echo 'export PATH=/home/jxdong/biosoft/htslib-1.9/bin:$PATH' >>~/.bashrc

7)source ~/.bashrc

----------------------安装sratoolkit------------------------------------------------------------------------------

1）下载http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk

2）tar zxvf sratoolkit.2.9.2-centos_linux64/.tar.gz

3）mkdir sratoolkit.2.9.2-centos_linux64/  sratoolkit.2.9.2

4）添加环境变量 echo 'export PATH=/home/jxdong/biosoft/sratoolkit.2.9.2-centos_linux64/bin:$PATH' >> ~/.bashrc

5)source  ~/.bashrc

----------------------安装bedtools------------------------------------------------------------------------------

1）下载https://github.com/arq5x/bedtools2

##wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz

2）tar -zxvf bedtools-2.25.0.tar.gz

3) cd bedtools2/

3）make

4）添加环境变量 echo 'export PATH=/home/jxdong/biosoft/sratoolkit.2.9.2-centos_linux64/bin:$PATH' >> ~/.bashrc

5)source  ~/.bashrc

----------------------安装GATK------------------------------------------------------------------------------

1）下载https://software.broadinstitute.org/gatk/download/

2) unzip  gatk-4.0.7.0.zip

3)mv  gatk-4.0.7.0 GATK

4)  echo 'export PATH=/home/jxdong/biosoft/GATK:$PATH' >>~/.bashrc

5)soure ~/.bashrc

----------------------安装TrimGalore------------------------------------------------------------------------------

1）下载http://www.bioinformatics.babraham.ac.uk/projects/download.html#trim_galore

2) unzip TrimGalore-0.5.0.zip

3)mv TrimGalore-0.5.0/ TrimGalore

4)  echo 'export PATH=/home/jxdong/biosoft/TrimGalore:$PATH' >>~/.bashrc

5)soure ~/.bashrc

----------------------安装qualimap------------------------------------------------------------------------------

1）下载 https://bitbucket.org/kokonech/qualimap/downloads

2）unzip qualimap_v2.2.1.zip

3)mv qualimap_v2.2.1/ qualimap
4)cd qualimap

5)./qualimapp --help

----------------------安装vcftools------------------------------------------------------------------------------

1）下载https://vcftools.github.io/downloads.html
2）tar zxvf  vcftools-vcftools-v0.1.16-0-g93ec375.tar.gz
3)mv vcftools-vcftools-93ec375/ vcftool
4)export PERL5LIB=/home/jxdong/biosoft/vcftool/src/perl/
5)./autogen.sh
6)./configure --prefix=/home/jxdong/biosoft/vcftool/src
7)make
8)make install
9)echo 'PATH=/home/jxdong/biosoft/vcftool/src/bin/bin:$PATH' >>~/.bashrc
10)source ~/.bashrc
11)vcftools --help

---------------------------安装bwa------------------------------------------------------------------------------

1)下载https://sourceforge.net/projects/bio-bwa/
2）tar xvfj bwa-0.7.17.tar.bz2
3）mv bwa-0.7.17/ bwa
4）cd bwa
5) make
6) echo 'export PATH=/home/jxdong/biosoft/bwa:$PATH'  >> ~/.bashrc
7) source ~/.bashrc

---------------------------安装deeptools------------------------------------------------------------------------------

1) https://files.pythonhosted.org/packages/54/7b/a0248f8a65468f399e7956fc79761f55ff785d86775466db0d16e7af163f/deepTools-3.1.2.tar.gz

2) tar -xzvf  deepTools-3.1.2.tar.gz

3) python setup.py install
4) echo 'export PATH=/home/jxdong/biosoft/deepTools-3.1.2:$PATH'

---------------------------安装sratoolkit------------------------------------------------------------------------------

1）https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz

2）sratoolkit.current-ubuntu64.tar.gz

3）echo 'export PATH=/home/jxdong/biosoft/sratoolkit/bin:$PATH' >>~/.bashrc

------------------------------------ 安装homer------------------------------------------------------

1) mkdir homer && cd homer

2)wget http://homer.salk.edu/homer/configureHomer.pl

3)perl configureHomer.pl -install

4) echo 'export PATH=/home/jxdong/biosoft/homer/bin:$PATH' >>~/.bashrc

5)source ~/.bashrc

------------------------------------ 安装homer------------------------------------------------------

------------------------------------ 安装meme-----------------------------------------------------

1) wget http://meme-suite.org/meme-software/5.0.1/meme_5.0.1.tar.gz

2) tar -xzvf meme_5.0.1.tar.gz

3) ./configure --prefix=/usr/bin  --with-url=http://meme-suite.org  --enable-build-libxml2   --enable-build-libxslt

4)make

5)makemakemake test

6)make install

 

-------------------------------------  安装MACS2MACS2(这个软件必须是python2)-------------------------------------------------

1) wget https://files.pythonhosted.org/packages/9f/99/a8ac96b357f6b0a6f559fe0f5a81bcae12b98579551620ce07c5183aee2c/MACS2-2.1.1.20160309.tar.gz

2）tar -xzvf  MACS2-2.1.1.20160309.tar.gz

t ar -xzvf

3) z