生物信息学常见1000个软件的安装代码！

安装软件是入行生物信息学着最常见的坑，毕竟你不得不用别人写的工具，但是写工具的人的水平参差不齐，所以必然有些难以安装，有些简单。

但是一定安装软件超过一定次数，你再回过头来看，就会觉得是非常简单的。我这里把我安装的软件的所有代码全部共享出来，理论上，你只要是linux或者mac，就用我的代码就可以复现一下。

## annovar and GATK

## Download and install sratoolkit

## http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

## http://www.ncbi.nlm.nih.gov/books/NBK158900/

cd ~/biosoft

mkdir sratoolkit && cd sratoolkit

wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.6.3/sratoolkit.2.6.3-centos_linux64.tar.gz

## Length: 63453761 (61M) [application/x-gzip]

## Saving to: "sratoolkit.2.6.3-centos_linux64.tar.gz"

tar zxvf sratoolkit.2.6.3-centos_linux64.tar.gz

~/biosoft/sratoolkit/sratoolkit.2.6.3-centos_linux64/bin/fastdump -h

mkdir -p ~/biosoft/myBin

echo 'export PATH=/home/jianmingzeng/biosoft/myBin/bin:$PATH' >>~/.bashrc

source ~/.bashrc

cd ~/biosoft

mkdir cmake && cd cmake

wget http://cmake.org/files/v3.3/cmake-3.3.2.tar.gz

tar xvfz cmake-3.3.2.tar.gz

cd cmake-3.3.2

./configure --prefix=/home/jianmingzeng/biosoft/myBin

make

make install

## Download and install samtools

## http://samtools.sourceforge.net/

## http://www.htslib.org/doc/samtools.html

cd ~/biosoft

mkdir samtools && cd samtools

wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2

tar xvfj samtools-1.3.1.tar.bz2

cd samtools-1.3.1

./configure --prefix=/home/jianmingzeng/biosoft/myBin

make

make install

~/biosoft/myBin/bin/samtools --help

~/biosoft/myBin/bin/plot-bamstats --help

cd htslib-1.3.1

./configure --prefix=/home/jianmingzeng/biosoft/myBin

make

make install

~/biosoft/myBin/bin/tabix

# ## Download and install tabix

# cd ~/biosoft

# mkdir tabix && cd tabix

# # http://genometoolbox.blogspot.com/2013/11/installing-tabix-on-unix.html

# tar xvfj tabix-0.2.6.tar.bz2

# cd tabix-0.2.6

# make

# cd ~/biosoft

# ## http://samtools.github.io/bcftools/

# mkdir htslib && cd htslib

# git clone git://github.com/samtools/htslib.git

# cd htslib

# make

## Download and install bcftools

## http://www.htslib.org/download/

## http://www.htslib.org/doc/bcftools-1.0.html

cd ~/biosoft

mkdir bcftools && cd bcftools

wget https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2

tar xvfj bcftools-1.3.1.tar.bz2

cd bcftools-1.3.1

make

cp bcftools /home/jianmingzeng/biosoft/myBin

~/biosoft/myBin/bin/bcftools --help

## Download and install vcftools

## https://vcftools.github.io/index.html

## http://vcftools.sourceforge.net/specs.html

cd ~/biosoft

mkdir vcftools && cd vcftools

# wget https://codeload.github.com/vcftools/vcftools/legacy.zip/master -O vcftools-vcftools-v0.1.14-24-gac1bfd5.zip

# unzip vcftools-vcftools-v0.1.14-24-gac1bfd5.zip

# mv vcftools-vcftools-ac1bfd5 vcftools-v0.1.14-24

# cd vcftools-v0.1.14-24

# export PERL5LIB=/home/jianmingzeng/biosoft/vcftools/vcftools-v0.1.14-24/src/perl/

# ./autogen.sh

# ./configure --prefix=/home/jianmingzeng/biosoft/myBin

# make

# make install

# ~/biosoft/myBin/bin/vcftools --help

wget https://sourceforge.net/projects/vcftools/files/vcftools_0.1.13.tar.gz

tar zxvf vcftools_0.1.13.tar.gz

cd vcftools_0.1.13

make

## Download and install ANNOVAR

cd ~/biosoft

# The latest version of ANNOVAR (2016Feb01) can be downloaded here (registration required)

# http://www.openbioinformatics.org/annovar/annovar_download_form.php

mkdir ANNOVAR && cd ANNOVAR

## Download and install samstat

## http://samstat.sourceforge.net/

## http://www.htslib.org/doc/samtools.html

cd ~/biosoft

mkdir samstat && cd samstat

wget http://liquidtelecom.dl.sourceforge.net/project/samstat/samstat-1.5.tar.gz

tar zxvf samstat-1.5.tar.gz

cd samstat-1.5

./configure --prefix=/home/jianmingzeng/biosoft/myBin

make

make install

~/biosoft/myBin/bin/samstat --help

## Download and install picardtools

## https://sourceforge.net/projects/picard/

## https://github.com/broadinstitute/picard

cd ~/biosoft

mkdir picardtools && cd picardtools

wget http://ncu.dl.sourceforge.net/project/picard/picard-tools/1.119/picard-tools-1.119.zip

unzip picard-tools-1.119.zip

## Download and install freebayes

## https://github.com/ekg/freebayes

## http://clavius.bc.edu/~erik/CSHL-advanced-sequencing/freebayes-tutorial.html

cd ~/biosoft

mkdir freebayes && cd freebayes

## wget -O freebayes-master.zip https://codeload.github.com/ekg/freebayes/zip/master

## unzip freebayes-master.zip

wget http://clavius.bc.edu/~erik/freebayes/freebayes-5d5b8ac0.tar.gz

tar xzvf freebayes-5d5b8ac0.tar.gz

cd freebayes

make

~/biosoft/freebayes/freebayes/bin/freebayes

cd ~/biosoft

## https://sourceforge.net/projects/varscan/files/

## http://varscan.sourceforge.net/index.html

mkdir VarScan && cd VarScan

wget https://sourceforge.net/projects/varscan/files/VarScan.v2.3.9.jar

cd ~/biosoft

mkdir SnpEff && cd SnpEff

## http://snpeff.sourceforge.net/

## http://snpeff.sourceforge.net/SnpSift.html

## http://snpeff.sourceforge.net/SnpEff_manual.html

wget http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip

## java -jar snpEff.jar download GRCh37.75

## java -Xmx4G -jar snpEff.jar -i vcf -o vcf GRCh37.75 example.vcf > example_snpeff.vcf

unzip snpEff_latest_core.zip

## https://github.com/najoshi/sickle

cd ~/biosoft

mkdir sickle && cd sickle

wget https://codeload.github.com/najoshi/sickle/zip/master -O sickle.zip

unzip sickle.zip

cd sickle-master

make

~/biosoft/sickle/sickle-master/sickle -h

cd ~/biosoft

## http://www.usadellab.org/cms/?page=trimmomatic

## http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf

mkdir Trimmomatic && cd Trimmomatic

wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip

unzip Trimmomatic-0.36.zip

java -jar ~/biosoft/Trimmomatic/Trimmomatic-0.36/trimmomatic-0.36.jar -h

## Download and install bedtools

cd ~/biosoft

mkdir bedtools && cd bedtools

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

## Length: 19581105 (19M) [application/octet-stream]

tar -zxvf bedtools-2.25.0.tar.gz

cd bedtools2

make

#~/biosoft/bedtools/bedtools2/bin/

## Download and install PeakRanger

cd ~/biosoft

mkdir PeakRanger && cd PeakRanger

wget https://sourceforge.net/projects/ranger/files/PeakRanger-1.18-Linux-x86_64.zip

## Length: 1517587 (1.4M) [application/octet-stream]

unzip PeakRanger-1.18-Linux-x86_64.zip

~/biosoft/PeakRanger/bin/peakranger -h

## Download and install bowtie

cd ~/biosoft

mkdir bowtie && cd bowtie

wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip

#Length: 27073243 (26M) [application/octet-stream]

#Saving to: "download" ## I made a mistake here for downloading the bowtie2

mv download bowtie2-2.2.9-linux-x86_64.zip

unzip bowtie2-2.2.9-linux-x86_64.zip

## Download and install BWA

cd ~/biosoft

mkdir bwa && cd bwa

#http://sourceforge.net/projects/bio-bwa/files/

wget https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.15.tar.bz2

tar xvfj bwa-0.7.15.tar.bz2 # x extracts, v is verbose (details of what it is doing), f skips prompting for each individual file, and j tells it to unzip .bz2 files

cd bwa-0.7.15

make

#export PATH=$PATH:/path/to/bwa-0.7.15 # Add bwa to your PATH by editing ~/.bashrc file (or .bash_profile or .profile file)

# /path/to/ is an placeholder. Replace with real path to BWA on your machine

#source ~/.bashrc

## Download and install macs2

## // https://pypi.python.org/pypi/MACS2/

cd ~/biosoft

mkdir macs2 && cd macs2

## just stick to PyPI release: https://pypi.python.org/pypi/MACS2

wget https://pypi.python.org/packages/9f/99/a8ac96b357f6b0a6f559fe0f5a81bcae12b98579551620ce07c5183aee2c/MACS2-2.1.1.20160309.tar.gz -O MACS2-2.1.1.tar.gz

tar zxvf MACS2-2.1.1.tar.gz

cd MACS2-2.1.1.20160309/

python setup.py install --user

## https://docs.python.org/2/install/

~/.local/bin/macs2 --help

#wget https://codeload.github.com/taoliu/MACS/zip/master -O MACS-master.zip

#unzip MACS-master.zip

#cd MACS-master

## So you can't just pull github snapshot then run setup.py to install MACS2. Instead

# ImageMagick

cd ~/biosoft

mkdir ImageMagick && cd ImageMagick

## http://www.imagemagick.org/

cd ~/biosoft

mkdir weblogo && cd weblogo

## http://weblogo.berkeley.edu/

wget http://weblogo.berkeley.edu/release/weblogo.2.8.2.tar.gz

tar zxvf weblogo.2.8.2.tar.gz

cd weblogo

export PATH=$PATH:/home/jianmingzeng/biosoft/weblogo/weblogo

source ~/.bashrc

cd ~/biosoft

mkdir Ghostscript && cd Ghostscript

# http://www.ghostscript.com/download/gsdnld.html

# http://www.ghostscript.com/doc/9.20/Readme.htm

wget https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs920/ghostscript-9.20-linux-x86_64.tgz

tar zxvf ghostscript-9.20-linux-x86_64.tgz

cp ghostscript-9.20-linux-x86_64/gs-920-linux_x86_64 ~/biosoft/myBin/bin/gs

## make sure the "gs" program is executable

## Download and install homer (Hypergeometric Optimization of Motif EnRichment)

## // http://homer.salk.edu/homer/

## // http://blog.qiubio.com:8080/archives/3024

## The commands gs, seqlogo, blat, and samtools should now work from the command line

cd ~/biosoft

mkdir homer && cd homer

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

perl configureHomer.pl -install

perl configureHomer.pl -install hg19

## Download and install SWEMBL

cd ~/biosoft

mkdir SWEMBL && cd SWEMBL

#### readme: http://www.ebi.ac.uk/~swilder/SWEMBL/beginners.html

wget http://www.ebi.ac.uk/~swilder/SWEMBL/SWEMBL.3.3.1.tar.bz2

tar xvfj SWEMBL.3.3.1.tar.bz2

cd SWEMBL.3.3.1/

make

## error

## Download and install SISSRs

cd ~/biosoft

mkdir SISSRs && cd SISSRs

#### readme: https://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/SISSRs-Manual.pdf

wget http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/sissrs_v1.4.tar.gz

tar xzvf sissrs_v1.4.tar.gz

~/biosoft/SISSRs/sissrs.pl

## Download and install SISSRs

cd ~/biosoft

mkdir QuEST && cd QuEST

#### http://mendel.stanford.edu/SidowLab/downloads/quest/

wget http://mendel.stanford.edu/SidowLab/downloads/quest/QuEST_2.4.tar.gz

tar xzvf QuEST_2.4.tar.gz

cd QuEST_2.4

## Download and install fastqc

cd ~/biosoft

mkdir fastqc && cd fastqc

wget http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/fastqc_v0.11.5.zip

unzip fastqc_v0.11.5.zip

## Download and install CEAS

## http://liulab.dfci.harvard.edu/CEAS/download.html

cd ~/biosoft

mkdir CEAS && cd CEAS

wget http://liulab.dfci.harvard.edu/CEAS/src/CEAS-Package-1.0.2.tar.gz

tar zxvf CEAS-Package-1.0.2.tar.gz

cd CEAS-Package-1.0.2

python setup.py install --user

## http://liulab.dfci.harvard.edu/CEAS/usermanual.html

~/.local/bin/ceas --help

mkdir annotation && cd annotation

wget http://liulab.dfci.harvard.edu/CEAS/src/hg19.refGene.gz ; gunzip hg19.refGene.gz

# http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz ## gunzip refGene.txt.gz ; mv refGene.txt hg19refGene.txt

## Download and install CEAS

## http://liulab.dfci.harvard.edu/CEAS/download.html

cd ~/biosoft

mkdir crossmap && cd crossmap

pip install CrossMap --user

## http://crossmap.sourceforge.net/#use-pip-to-install-crossmap

mkdir chain_files && cd chain_files

wget http://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToMm9.over.chain.gz

wget http://hgdownload.soe.ucsc.edu/goldenPath/mm9/liftOver/mm9ToMm10.over.chain.gz

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz

# http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz ## gunzip refGene.txt.gz ; mv refGene.txt hg19refGene.txt

# Usage: CrossMap.py bed ~/biosoft/crossmap/chain_files/mm9ToMm10.over.chain.gz test.mm9.bed3

cd ~/biosoft

# http://www.broadinstitute.org/cancer/cga/rnaseqc_run

# http://www.broadinstitute.org/cancer/cga/rnaseqc_download

mkdir RNA-SeQC && cd RNA-SeQC

#### readme: http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/rnaseqc/RNA-SeQC_Help_v1.1.2.pdf

wget http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar

#TopHat+Cufflinks+ pipeline

## Download and install TopHat

# https://ccb.jhu.edu/software/tophat/index.shtml

cd ~/biosoft

mkdir TopHat && cd TopHat

#### readme: https://ccb.jhu.edu/software/tophat/manual.shtml

wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz

tar xzvf tophat-2.1.1.Linux_x86_64.tar.gz

ln -s tophat-2.1.1.Linux_x86_64 current

# ~/biosoft/TopHat/current/tophat2

## Download and install Cufflinks

# http://cole-trapnell-lab.github.io/cufflinks/

cd ~/biosoft

mkdir Cufflinks && cd Cufflinks

#### readme: http://cole-trapnell-lab.github.io/cufflinks/manual/

#### install:http://cole-trapnell-lab.github.io/cufflinks/install/

wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz

tar xzvf cufflinks-2.2.1.Linux_x86_64.tar.gz

ln -s cufflinks-2.2.1.Linux_x86_64 current

~/biosoft/Cufflinks/current/cufflinks

#HISAT-Stringtie2-Ballgown pipeline

## Download and install HISAT

# https://ccb.jhu.edu/software/hisat2/index.shtml

cd ~/biosoft

mkdir HISAT && cd HISAT

#### readme: https://ccb.jhu.edu/software/hisat2/manual.shtml

wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.4-Linux_x86_64.zip

unzip hisat2-2.0.4-Linux_x86_64.zip

ln -s hisat2-2.0.4 current

## ~/biosoft/HISAT/current/hisat2-build

## ~/biosoft/HISAT/current/hisat2

## Download and install StringTie

## https://ccb.jhu.edu/software/stringtie/ ## https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual

cd ~/biosoft

mkdir StringTie && cd StringTie

wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.2.3.Linux_x86_64.tar.gz

tar zxvf stringtie-1.2.3.Linux_x86_64.tar.gz

ln -s stringtie-1.2.3.Linux_x86_64 current

# ~/biosoft/StringTie/current/stringtie

cd ~/biosoft

mkdir RSEM && cd RSEM

wget https://codeload.github.com/deweylab/RSEM/tar.gz/v1.2.31

mv v1.2.31 RSEM.v1.2.31.tar.gz

tar zxvf RSEM.v1.2.31.tar.gz

## Download and install HTSeq

## http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html

## https://pypi.python.org/pypi/HTSeq

cd ~/biosoft

mkdir HTSeq && cd HTSeq

wget https://pypi.python.org/packages/72/0f/566afae6c149762af301a19686cd5fd1876deb2b48d09546dbd5caebbb78/HTSeq-0.6.1.tar.gz

tar zxvf HTSeq-0.6.1.tar.gz

cd HTSeq-0.6.1

python setup.py install --user

~/.local/bin/htseq-count --help

## ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M1/

## http://hgdownload-test.cse.ucsc.edu/goldenPath/mm10/liftOver/

## GRCm38/mm10 (Dec, 2011)

## ls *bam |while read id;do ( ~/.local/bin/htseq-count -f bam $id genecode/mm9/gencode.vM1.annotation.gtf.gz 1>${id%%.*}.gene.counts ) ;done

## ls *bam |while read id;do ( ~/.local/bin/htseq-count -f bam -i exon_id $id genecode/mm9/gencode.vM1.annotation.gtf.gz 1>${id%%.*}.exon.counts ) ;done

## Download and install kallisto

## https://pachterlab.github.io/kallisto/starting

cd ~/biosoft

mkdir kallisto && cd kallisto

wget https://github.com/pachterlab/kallisto/releases/download/v0.43.0/kallisto_linux-v0.43.0.tar.gz

#tar zxvf

## Download and install Sailfish

## http://www.cs.cmu.edu/~ckingsf/software/sailfish/ ##

cd ~/biosoft

mkdir Sailfish && cd Sailfish

wget https://github.com/kingsfordgroup/sailfish/releases/download/v0.9.2/SailfishBeta-0.9.2_DebianSqueeze.tar.gz

#tar zxvf

## Download and install salmon

## http://salmon.readthedocs.io/en/latest/salmon.html ##

cd ~/biosoft

mkdir salmon && cd salmon

## https://github.com/COMBINE-lab/salmon

#tar zxvf

cd ~/biosoft

mkdir GDC && cd GDC

# https://gdc.cancer.gov/access-data/gdc-data-transfer-tool

# http://gdc-docs.nci.nih.gov/Data_Transfer_Tool/Users_Guide/Getting_Started/

wget https://gdc.nci.nih.gov/files/public/file/gdc-client_v1.2.0_Ubuntu14.04_x64.zip

unzip gdc-client_v1.2.0_Ubuntu14.04_x64.zip

cd ~/biosoft/myBin/bin

## http://hgdownload.cse.ucsc.edu/admin/exe/

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedSort

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfClient

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfServer

## Download and install variationtoolkit

## https://code.google.com/archive/p/variationtoolkit/downloads

cd ~/biosoft

mkdir variationtoolkit && cd variationtoolkit

wget https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/variationtoolkit/archive.tar.gz

tar zxvf archive.tar.gz

cd variationtoolkit

make

## Download and install transvar

# http://bioinformatics.mdanderson.org/main/Transvar

cd ~/biosoft

# https://bitbucket.org/wanding/transvar

mkdir transvar && cd transvar

wget https://bitbucket.org/wanding/transvar/get/v2.1.19.20160221.zip

unzip v2.1.19.20160221.zip

cd wanding-transvar-5dd8a7366999

python setup.py install --user

cd ~/biosoft

# http://kobas.cbi.pku.edu.cn/download.php

mkdir kobas && cd kobas

# wget http://kobas.cbi.pku.edu.cn/download_file.php?type=seq_pep&filename=hsa.pep.fasta.gz

# wget http://kobas.cbi.pku.edu.cn/download_file.php?type=sqlite3&filename=hsa.db.gz

wget http://kobas.cbi.pku.edu.cn/kobas-2.1.1/kobas-2.1.1.tar.gz

tar zxvf kobas-2.1.1.tar.gz

cd kobas-2.1.1_20160822

# * Download the KOBAS organism data package (organism.db.gz) from KOBAS Backend databases download website

# * Download the KOBAS specific species data package from KOBAS Backend databases download website (for example, hsa.db.gz)

# * Download the specific sequence file from KOBAS sequence files download website (for example, hsa.pep.fasta.gz)

# * `gunzip organism.db.gz`

# * `gunzip hsa.db.gz`

# * Move all databases into ${kobas_home}/sqlite3/ (for example, organism.db, hsa.db)

# * `gunzip hsa.pep.fasta.gz`

# * Move the fasta sequence file into ${kobas_home}/seq_pep/

# * `makeblastdb -in hsa.pep.fasta -dbtype prot`

pip install RPy2 --user

pip install Numpy --user

pip install Pandas --user

pip install BioPython --user

pip install matplotlib --user

pip install PySQLite --user

source("http://bioconductor.org/biocLite.R")

biocLite("qvalue")

## Download and install bamtools

## https://github.com/pezmaster31/bamtools/wiki/Building-and-installing

cd ~/biosoft

mkdir bamtools && cd bamtools

git clone git://github.com/pezmaster31/bamtools.git

cd bamtools

cmake --version ## BamTools requires CMake (version >= 2.6.4).

mkdir build && cd build

cmake ../

make

~/biosoft/bamtools/bamtools/bin/bamtools

## Download and install BAMStats

## http://bamstats.sourceforge.net/

## https://sourceforge.net/projects/bamstats/files/

cd ~/biosoft

mkdir BAMStats && cd BAMStats

wget https://nchc.dl.sourceforge.net/project/bamstats/BAMStats-1.25.zip

unzip BAMStats-1.25.zip

#java -jar ~/biosoft/BAMStats/BAMStats-1.25/BAMStats-1.25.jar --help

## Download and install Qualimap

## http://qualimap.bioinfo.cipf.es/

cd ~/biosoft

mkdir Qualimap && cd Qualimap

wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1.zip

## readme http://qualimap.bioinfo.cipf.es/doc_html/index.html

## example results :http://kokonech.github.io/qualimap/HG00096.chr20_bamqc/qualimapReport.html

unzip qualimap_v2.2.1.zip

~/biosoft/bamtools/bamtools/bin/bamtools

~/biosoft/Qualimap/qualimap_v2.2.1/qualimap --help ## --java-mem-size=4G

## modify ~/.bashrc by adding PATH=$PATH:~/.local/bin/

## Download and install deepTools

## https://github.com/fidelram/deepTools

## http://deeptools.readthedocs.io/en/latest/content/example_usage.html

pip install pyBigWig --user

cd ~/biosoft

mkdir deepTools && cd deepTools

git clone https://github.com/fidelram/deepTools ## 130M,

cd deepTools

python setup.py install --user

## 17 tools in ~/.local/bin/

~/.local/bin/deeptools

cd ~/biosoft

mkdir ngsplot && cd ngsplot

## download by yourself :https://drive.google.com/drive/folders/0B1PVLadG_dCKN1liNFY0MVM1Ulk

tar -zxvf ngsplot-2.61.tar.gz

tar zxvf ngsplot.eg.bam.tar.gz

echo 'export PATH=/home/jianmingzeng/biosoft/ngsplot/ngsplot/bin:$PATH' >>~/.bashrc

echo 'export NGSPLOT=/home/jianmingzeng/biosoft/ngsplot/ngsplot' >>~/.bashrc

source ~/.bashrc

install.packages("doMC", dep=T)

install.packages("caTools", dep=T)

install.packages("utils", dep=T)

source("http://bioconductor.org/biocLite.R")

biocLite( "BSgenome" )

biocLite( "Rsamtools" )

biocLite( "ShortRead" )

cd ~/biosoft

mkdir breakdancer && cd breakdancer

# http://breakdancer.sourceforge.net/

# you need to install 2 perl module by yourself : http://breakdancer.sourceforge.net/moreperl.html

wget https://sourceforge.net/projects/breakdancer/files/breakdancer-1.1.2_2013_03_08.zip

unzip breakdancer-1.1.2_2013_03_08.zip

cd breakdancer-1.1.2/cpp

make ##something wrong !

## usage: http://breakdancer.sourceforge.net/pipeline.html

cd ~/biosoft

# http://boevalab.com/FREEC/

mkdir Control-FREEC && cd Control-FREEC

# https://github.com/BoevaLab/FREEC/releases

wget https://github.com/BoevaLab/FREEC/archive/v10.3.zip

unzip v10.3.zip

# https://www.ncbi.nlm.nih.gov/pubmed/22155870

# http://boevalab.com/FREEC/tutorial.html

# http://samtools.sourceforge.net/pileup.shtml

cd ~/biosoft

# https://github.com/dellytools/delly

mkdir delly && cd delly

# git clone --recursive https://github.com/dellytools/delly.git

# cd delly

# make all

# make PARALLEL=1 -B src/delly

wget https://github.com/dellytools/delly/releases/download/v0.7.6/delly_v0.7.6_linux_x86_64bit

chmod 777 delly_v0.7.6_linux_x86_64bit

~/biosoft/delly/delly_v0.7.6_linux_x86_64bit --help

## delly call -t DEL -g hg19.fa -o s1.bcf -x hg19.excl sample1.bam

## ./delly/src/bcftools/bcftools view delly.bcf > delly.vcf

## The SV type can be DEL, DUP, INV, TRA, or INS for deletions, tandem duplications, inversions, translocations and small insertions, respectively.

## In addition, you can filter input reads more stringently using -q 20 and -s 15.

cd ~/biosoft

# https://www.cog-genomics.org/plink2/data#merge_list

mkdir PLINK && cd PLINK

wget https://www.cog-genomics.org/static/bin/plink170113/plink_linux_x86_64.zip

unzip plink_linux_x86_64.zip

~/biosoft/PLINK/plink

## Download and install Scalpel

cd ~/biosoft

mkdir Scalpel && cd Scalpel

wget https://downloads.sourceforge.net/project/scalpel/scalpel-0.5.3.tar.gz

tar zxvf scalpel-0.5.3.tar.gz

cd scalpel-0.5.3

make

~/biosoft/Scalpel/scalpel-0.5.3/scalpel-discovery --help

~/biosoft/Scalpel/scalpel-0.5.3/scalpel-export --help

cd ~/biosoft

# https://www.cog-genomics.org/plink2/data#merge_list

mkdir firehose && cd firehose

wget http://gdac.broadinstitute.org/runs/code/firehose_get_latest.zip

unzip firehose_get_latest.zip

~/biosoft/firehose/firehose_get

~/biosoft/firehose/firehose_get -tasks clinical analyses latest brca

cd ~/biosoft

# https://www.cog-genomics.org/plink2/data#merge_list

mkdir fastpop && cd fastpop

wget https://sourceforge.net/projects/fastpop/files/FastPop.tar.gz

wget https://jaist.dl.sourceforge.net/project/fastpop/FastPop_Instruction.pdf

tar zxvf FastPop.tar.gz

pip install cnvkit --user