【原创】包管理工具conda安装生信软件//课堂笔记

 wget -c https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh

bash Miniconda3-4.5.11-Linux-x86_64.sh

export PATH=/root/miniconda3/bin:$PATH     //no

source ~/miniconda3/bin/activate

添加频道：

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/

conda config --set show_channel_urls yes

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/

查看配置环境：

vim ~/.condarc

conda search bwa

conda install bwa -y

conda install samtools=1.8 -y

调用软件：

当前环境直接输软件名

echo $PATH

source deactivate

ln -s ~/miniconda3/bin/bwa /usr/local/sbin

用conda建立互不干扰的环境：

source ~/miniconda3/bin/activate

conda info --envs

conda create -n python2 python=2

conda activate python2

conda install macs2

删除一个环境

conda remove -n python2 --all

---

conda install fastqc trimmomatic

conda activate python2

conda install htseq //htseq-count

source deactivate 

conda install hisat2