1. 什么是Conda?2. 关于几个Conda3. Conda环境管理4. 安装Condawget -m https://mirrors.tuna./anaconda/archive/Anaconda3-5.3.1-Linux-x86_64.sh bash Anaconda3-5.3.1-Linux-x86_64.sh #安装下载的sh文件 5. 配置仓库镜像#一:官方频道 conda config --add channels bioconda conda config --add channels conda-forge conda config --set show_channel_urls yes #二:清华镜像频道 conda config --add channels https://mirrors.tuna./anaconda/pkgs/free/ conda config --add channels https://mirrors.tuna./anaconda/pkgs/main/ conda config --add channels https://mirrors.tuna./anaconda/cloud/conda-forge/ conda config --add channels https://mirrors.tuna./anaconda/cloud/bioconda/ conda config --set show_channel_urls yes #三:北外镜像频道 conda config --add channels https://mirrors./anaconda/pkgs/free/ conda config --add channels https://mirrors./anaconda/pkgs/main/ conda config --add channels https://mirrors./anaconda/cloud/conda-forge/ conda config --add channels https://mirrors./anaconda/cloud/bioconda/ conda config --set show_channel_urls yes conda config --set ssl_verify False 6. 创建conda小环境#base环境: source ~/anaconda3/bin/activate #conda activate /home/hucy/anaconda3 conda create -n SNPseq #创建名为SNPseq的conda小环境 #-n:指定环境名称 conda env list # 或 conda info --env # 列出已存在的小环境 conda activate SNPseq #启动SNPseq这个conda小环境 conda activate base #切换到base环境(确保安装在base) conda deactivate #退出SNPseq这个conda小环境 conda remove -n SNPseq --all #重命名小环境,例如将Python2重命名为py2 conda create -n Python2 conda create -n py2 --clone Python2 conda remove -n py2 --all 7. conda环境安装软件conda search fastqc #安装fastqc,加等号指定安装0.11.7版本的,也可以不指定 conda install fastqc=0.11.7 #加-y参数可以跳过确认步骤 conda install -y fastqc=0.11.7 #删除软件 conda remove fastqc #升级软件 conda update fastqc #升级conda自身 conda update conda conda install -c bioconda fastqc -y #fastqc --help conda install -c bioconda -c conda-forge multiqc #pip install multiqc conda install -c bioconda fastp -y #https://www.jianshu.com/p/10d8daa57d1d conda install -c bioconda fastx_toolkit -y #/home/hucy/anaconda3/envs/SNPseq/bin/fastx_clipper -h conda install -c bioconda solexaqa -y conda install -c bioconda trimmomatic -y conda install -c bioconda hisat2 -y #HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. conda install bwa -y conda install -c bioconda bowtie2 -y conda install samtools -y conda install -c bioconda picard -y conda install -c bioconda bedtools -y conda install -c bioconda snpeff -y conda install -c bioconda bcftools -y conda install -c bioconda freebayes -y conda install -c bioconda varscan -y conda install -c bioconda gatk -y conda install -c bioconda gatk4 -y # GenomeAnalysisTK -h 与gatk3 -h 显示结果一样 GenomeAnalysisTK -h gatk3 -h 8. 设置环境变量# 直接将conda的软件安装路径,写入.bashrc export PATH="/home/hucy/anaconda3/envs/SNPseq/bin:$PATH" #export是临时的,关闭终端就没有了,需写入~/.bashrc cp ~/.bashrc{,.bak} # 修改系统文件.bashrc前,可以先快速备份一下 vim ~/.bashrc # export PATH="/home/hucy/anaconda3/envs/SNPseq/bin:$PATH" source ~/.bashrc #载入修改后的环境 echo $PATH 9. 创建软链接mkdir ~/.soft #或创建一个文件夹,存储各种软件绝对路径的软链接,以便分享给Linux的其他用户 export PATH="/home/hucy/.soft:$PATH" #同理,可以将export PATH="/home/hucy/.soft:$PATH"写入root或者其他用户的.bashrc文件,以免重复安装过多软件。 which bwa #查找bwa的绝对路径 which samtools ln -s /home/hucy/anaconda3/envs/SNPseq/bin/fastqc ~/.soft #创建conda中已装软件的软链接 ln -s /home/hucy/anaconda3/envs/SNPseq/bin/multiqc ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/trimmomatic ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/SolexaQA++ ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/bwa ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/bowtie2 ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/hisat2 ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/samtools ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/bedtools ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/picard ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/bcftools ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/gatk3 ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/gatk4 ~/.soft # ln -s /home/hucy/anaconda3/envs/SNPseq/bin/GenomeAnalysisTK ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/varscan ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/freebayes ~/.soft ln -s /home/hucy/anaconda3/envs/SNPseq/bin/snpEff ~/.soft source ~/.bashrc # ln -s /home/hucy/anaconda3/envs/SNPseq/share/picard-2.18.29-0/picard.jar ~/.soft # ln -s /home/hucy/anaconda3/envs/SNPseq/share/snpeff-5.0-1/snpEff.jar ~/.soft # ln -s /home/hucy/anaconda3/envs/SNPseq/share/varscan-2.4.4-1/VarScan.jar ~/.soft 10. 其他软件安装# tar 解压缩命令详解 https://blog.csdn.net/example440982/article/details/51712973 # /home/hucy/biosoft/src wget -c http://www./annovar/download/--apply--/annovar.latest.tar.gz tar -zxvf ~/biosoft/src/annovar.latest.tar.gz -C ../ cd ~/biosoft/annovar/ perl /home/hucy/biosoft/annovar/annotate_variation.pl 11. 其他环境配置# 0表示没有权限,1表示可执行权限,2表示可写权限,4表示可读权限,然后将其相加。 alias condaBase='source ~/anaconda3/bin/activate' #重命名简化激活condaBase环境命令 export PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/hucy/.dotnet/tools:/usr/local/java/bin:.:~" export PATH="/home/hucy/anaconda3/envs/SNPseq/bin:$PATH" export PATH="/home/hucy/.soft:$PATH" # annovar 别名设置,简化命令行 vim ~/.bashrc alias convert2annovar.pl="/home/hucy/biosoft/annovar/convert2annovar.pl" alias annotate_variation.pl="/home/hucy/biosoft/annovar/annotate_variation.pl" alias table_annovar.pl="/home/hucy/biosoft/annovar/table_annovar.pl" alias coding_change.pl="/home/hucy/biosoft/annovar/coding_change.pl" alias retrieve_seq_from_fasta.pl="/home/hucy/biosoft/annovar/retrieve_seq_from_fasta.pl" alias variants_reduction.pl="/home/hucy/biosoft/annovar/variants_reduction.pl" source ~/.bashrc 12. conda其他应用12.1 版本控制和迁移conda list -n rnaseq --export > conda_rnaseq_list.txt # 输出文件格式:软件名=版本号=build # 安装导出的信息 conda create -n rna -file conda_rnaseq_list.txt conda env export -n rnaseq > rnaseq.yml # 根据导出的yml文件创建环境 conda env create -f rnaseq.yml # 根据导出的yml文件更新环境 conda env update -f rnaseq.yml # yml文件提供的信息更全面 12.2 删除没有用的包及更换镜像conda clean -p #更换镜像配置的时候记得先运行这一条 conda clean -i 12.3 将conda安装到指定位置mkdir -p ~/biosoft/samtools #使用-p参数指定安装位置 conda install -p ~/biosoft/samtools samtools 可重复的生信分析系列二:Conda的介绍 生信分析平台搭建(七):bioconda conda的安装与使用(2021-04-27更新) Linux基础:软件安装技巧–conda |
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