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20220519_生物信息平台搭建及生物信息软件安装
01 基础软件安装
代码语言：javascript
复制基础软件安装
============================================================================================
#java安装
apt-get install openjdk-8-jdk
sudo add-apt-repository ppa:webupd8team/java
apt update
apt install -y oracle-java8-installer
apt install -y zlib1g zlib1g.dev
apt install -y libboost-dev
#conda安装
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
source ~/.bashrc
#添加软件源
conda config --add channels bioconda
conda config --add channels conda-forge
#R与Rstudio安装
apt install -y r-base
https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.3.1093-amd64.deb
dpkg -i rstudio-1.3.1093-amd64.deb
02 常用生物信息软件安装
主要采用conda安装、apt安装、pip安装、docker安装以及软件源码安装方法
代码语言：javascript
复制常用生信软件安装
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#(1)三代组装软件falcon安装
conda install -c bioconda pb-assembly
#fc_run --help 验证安装成功
#--------------------------------------------------------------------------------
#(2)三代纠错软件ccs软件安装
conda install -c bioconda pbccs
#ccs --help 验证安装成功
#--------------------------------------------------------------------------------
#(3)基因组组装质量评估软件安装busco
conda install -c https://conda.anaconda.org/bioconda busco
#busco--help 验证安装成功
#--------------------------------------------------------------------------------
#(4)samtools 已安装
conda install -c bioconda samtools
#--------------------------------------------------------------------------------
#(5)bedtools 已安装
conda install -c bioconda
#--------------------------------------------------------------------------------
#(6)cutadapt 已安装
conda install cutadapt
#--------------------------------------------------------------------------------
#(7)trimmmomatic已安装
conda install -c bioconda trimmomatic
#--------------------------------------------------------------------------------
#(8) jellyfish安装
apt install -y jellyfish
#--------------------------------------------------------------------------------
#(9)rna-star 安装
apt install -y rna-star
#--------------------------------------------------------------------------------
#(10)bowtie2已安装
conda install -c bioconda bowtie2
#--------------------------------------------------------------------------------
#(11)bowtie已安装
conda install -c bioconda bowtie
#--------------------------------------------------------------------------------
#(12)STAR已安装
conda install -c bioconda star
#STAR --help验证安装成功
#--------------------------------------------------------------------------------
#(13)bwa已安装
conda install -c bioconda bwa
#--------------------------------------------------------------------------------
#(14)novoalign已安装
conda install -c bioconda novoalign
#--------------------------------------------------------------------------------
#(15)tophat已安装
conda install -c bioconda tophat
#--------------------------------------------------------------------------------
#(16)tophat2已安装
conda install -c bioconda tophat2
#--------------------------------------------------------------------------------
#(17)cufflinks 已安装
conda install -c bioconda cufflinks
#--------------------------------------------------------------------------------
#(18)FeatureCount&subread
#--------------------------------------------------------------------------------
#(19)Stringtie已安装
conda install -c bioconda stringtie
#--------------------------------------------------------------------------------
#(20)hisat2 安装
apt install -y hisat2
#--------------------------------------------------------------------------------
#(21)picard已安装
# wget -c https://github.com/broadinstitute/picard/releases/download/2.21.6/picard.jar
# java -jar /opt/Picard/picard.jar -h 验证是否安装成功
#--------------------------------------------------------------------------------
#(22)SRA Toolkit已安装
#https://www.jianshu.com/p/6a4855023330
#wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2-1/sratoolkit.2.8.2-1-ubuntu64.tar.gz
#--------------------------------------------------------------------------------
#(23)igv已安装
conda install -c bioconda igv
#--------------------------------------------------------------------------------
#(24) canu已安装
apt install -y canu
#--------------------------------------------------------------------------------
#(25) seqtk 已安装
conda install -c bioconda seqtk
#--------------------------------------------------------------------------------
#(26)seqkit 已安装
conda install -c bioconda seqkit
#--------------------------------------------------------------------------------
#(27)BEDOPS 已安装
apt-get install bedops
#--------------------------------------------------------------------------------
#(28)MACS2已安装
conda install -c bioconda macs2
# macs2 --help 验证安装成功
#--------------------------------------------------------------------------------
#(29) homer 已安装
conda install -c bioconda homer
#--------------------------------------------------------------------------------
#(30) blast
pip install blast
# blstn -help 验证安装成功
#--------------------------------------------------------------------------------
#(31)blat已安装
conda install -c bioconda blat
#--------------------------------------------------------------------------------
#(32)fastqc 已安装
conda install -c bioconda fastqc
#--------------------------------------------------------------------------------
#(33) clustalx已安装
apt install -y clustalx
#--------------------------------------------------------------------------------
#(34)tabix已安装
apt-get install tabix
#--------------------------------------------------------------------------------
#(35)mothur 已安装
apt-get install mothur
#--------------------------------------------------------------------------------
#(36)meme已安装
conda install -c bioconda meme
#--------------------------------------------------------------------------------
#(37)nucleoatac已安装
pip install nucleoatac
#--------------------------------------------------------------------------------
#(38) cnvkit 已安装
apt-get install cnvkit -y
#--------------------------------------------------------------------------------
#(39) augustus 已安装
apt-get install augustus -y
#--------------------------------------------------------------------------------
#(40) bamtools 已安装
apt-get install bamtools
#--------------------------------------------------------------------------------
#(41)varna已安装
apt-get install varna
#--------------------------------------------------------------------------------
#(42)mcl已安装
apt-get install mcl
#--------------------------------------------------------------------------------
#(43) mafft 已安装
apt-get install mafft -y
#--------------------------------------------------------------------------------
#(44) last-align 已安装
apt-get install last-align
#--------------------------------------------------------------------------------
#(45)muscle 已安装
apt-get install muscle
#--------------------------------------------------------------------------------
#(46)Gblocks 已安装
conda install -c bioconda gblocks
#Gblocks --help 验证是否安装成功
#--------------------------------------------------------------------------------
#(47)paml以安装
conda install -c bioconda paml
#输入baseml验证是否安装成功
#--------------------------------------------------------------------------------
#(48)jModelTest已安装
apt-get install jmodeltest
#--------------------------------------------------------------------------------
#(49)phylip 已安装
apt-get install phylip
#--------------------------------------------------------------------------------
#(50)phyml 已安装
apt-get install phyml
#--------------------------------------------------------------------------------
#(51)RAxML已安装
apt-get install raxml
#raxmlHPC -h 验证安装成功
#--------------------------------------------------------------------------------
#(52)GARLI已安装
apt-get install garli
#--------------------------------------------------------------------------------
#(53)FastTree已安装
apt-get install fasttree
#--------------------------------------------------------------------------------
#(54)MrBayes已安装
apt-get install mrbayes
#输入mb --help验证安装成功
#--------------------------------------------------------------------------------
#(55)fastx-toolkit已安装成功
apt install fastx-toolkit
#输入fastq_quality_filter -h验证安装成功
#--------------------------------------------------------------------------------
#(56)minimap2已安装
conda install -c bioconda minimap2
#--------------------------------------------------------------------------------
#(57)bcftools已安装
apt-get install bcftools
#--------------------------------------------------------------------------------
#(58) khmer已安装
apt-get install khmer
#--------------------------------------------------------------------------------
#(59)spades已安装
apt-get install spades
#--------------------------------------------------------------------------------
#(60)velvet已安装
pip install velvet
#velveth -h验证安装成功
#--------------------------------------------------------------------------------
#(61)supernova 已安装
pip install supernova
#--------------------------------------------------------------------------------
#(62)kmergenie已安装
conda install -c bioconda kmergenie
#--------------------------------------------------------------------------------
#(63)oases已安装
conda install oases
#--------------------------------------------------------------------------------
#(64)mira-assembler已安装
apt-get install mira-assembler
# mira -h验证安装成功
#--------------------------------------------------------------------------------
#(65)nanopolish 已安装
apt-get install nanopolish -y
#--------------------------------------------------------------------------------
#(66)Racon已安装
conda install -c bioconda racon
#--------------------------------------------------------------------------------
#(67)pilon 已安装
conda install -c bioconda pilon
#--------------------------------------------------------------------------------
#(68)hmmer已安装
apt-get install hmmer
#hmmsearch --help 验证安装成功
#--------------------------------------------------------------------------------
#(69)prodigal 已安装
apt-get install prodigal
#--------------------------------------------------------------------------------
#(70)RNAmmer已安装
# http://www.cbs.dtu.dk/services/RNAmmer/
#--------------------------------------------------------------------------------
#(71)Circos已安装
apt-get install circos
#--------------------------------------------------------------------------------
#(72)FastANI已安装
# https://chk.ipmb.sinica.edu.tw/wiki/doku.php/computers/bioinfo_server_configuration#trim
# wget https://github.com/ParBLiSS/FastANI/releases/download/v1.1/fastani-Linux64-v1.1.zip
# /opt/FastANI
#--------------------------------------------------------------------------------
#(73) tbl2asn已安装
#wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
#chmod 755 linux64.tbl2asn
#linux64.tbl2asn -h 验证安装成功
#--------------------------------------------------------------------------------
#(74)TMHMM已安装
#https://chk.ipmb.sinica.edu.tw/wiki/doku.php/computers/bioinfo_server_configuration#trim
# /opt/TMHMM/tmhmm-2.0c/bin
#usage: cat sequence.fasta |tmhmm
#--------------------------------------------------------------------------------
#(75)SignalP已安装
# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp 从网站上下载解压之后，可
以直接调用
#--------------------------------------------------------------------------------
#(76)flye 已安装
conda install -c bioconda flye -y
#--------------------------------------------------------------------------------
#(78)miniasm 已安装
conda install -c bioconda miniasm -y
#--------------------------------------------------------------------------------
#(79)UCSCtools已安装下载
#/opt/UCSCtools
#nohup rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ ./ &
#--------------------------------------------------------------------------------
#(80) vnc4server已安装
# https://www.jianshu.com/p/a64e1bf1ee87
apt-get install vnc4server
#--------------------------------------------------------------------------------
#(81)RSeQC 已安装
pip install rseqc
#bam_stat.py -h验证安装成功
#--------------------------------------------------------------------------------
#(82) megahit 已安装
conda install -c bioconda -y megahit
#--------------------------------------------------------------------------------
#(83)VARNA已安装
wget -c http://varna.lri.fr/bin/VARNAv3-93.jar
#--------------------------------------------------------------------------------
#(84)JTKcycle已安装
wget http://www.openwetware.org/images/8/88/JTKversion3.zip
#--------------------------------------------------------------------------------
#(85)CIMS已安装
git clone https://github.com/chaolinzhanglab/czplib.git
git clone https://github.com/chaolinzhanglab/ctk.git
#--------------------------------------------------------------------------------
#(86)wtdbg2已安装
#git clone https://github.com/ruanjue/wtdbg2
#cd wtdbg2 && make
#echo 'export PATH=/home/share/biosoft/wtdbg2:$PATH' >> ~/.bashrc
#source ~/.bashrc
#--------------------------------------------------------------------------------
#(87) quast 已安装
conda install -c bioconda quast -y
#--------------------------------------------------------------------------------
#(88)eggnog-mapper 已安装
conda install -c bioconda eggnog-mapper -y
#--------------------------------------------------------------------------------
#(89)orthofinder 已安装
conda install -c bioconda orthofinder -y
#orthofinder -h验证是否安装成功
#--------------------------------------------------------------------------------
#(90)trinity 已安装
conda install -c bioconda trinity
#--------------------------------------------------------------------------------
#(91) rsem 已安装
conda install -c bioconda rsem -y
#--------------------------------------------------------------------------------
#(92) multiqc 已安装
conda install -c bioconda multiqc -y
#--------------------------------------------------------------------------------
#(93) sratools 已安装
conda install -c bioconda sratools -y
#--------------------------------------------------------------------------------
#(94)gfatools 已安装
conda install -c bioconda gfatools -y
#--------------------------------------------------------------------------------
#(95) Lachesis 已安装
docker pull aakashsur/lachesis
#--------------------------------------------------------------------------------
#(96)tailseeker 已安装
docker pull hyeshik/tailseeker
#--------------------------------------------------------------------------------
#(97)HiC-Pro 已安装
docker pull aryeelab/hicpro
#--------------------------------------------------------------------------------
#(98)mfold 已安装
docker pull pgcbioinfo/mfold
#--------------------------------------------------------------------------------
#(99)quickmerge已安装
sudo su
conda create -n quickmerge_env python=2
source activate quickmerge_env
git clone https://github.com/mahulchak/quickmerge.git
cd quickmerge/merger
make
cd ../MUMmer3.23
make check
make install
cd ../merger
最后将merger文件夹路径添加到./basrhrc 文件内的环境变量中
#--------------------------------------------------------------------------------
#(100) BUSCO已安装
conda create -n py2_env python=2
source activate py2_env 或 conda activate py2_env
conda install -c bioconda busco
export AUGUSTUS_CONFIG_PATH=/opt/ANACONDA/anaconda3/envs/py2_env/config/
run_busco -h 验证是否安装成功
