用bioconda 安装软件很方便
先安装miniconda

安装软件

#添加 bioconda 源
conda config --add channels bioconda
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/noarch
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/linux-64
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/noarch
conda config --add channels https://conda.anaconda.org/bioconda/linux-64
conda config --add channels https://conda.anaconda.org/bioconda/noarch
conda config --add channels https://conda.anaconda.org/conda-forge/linux-64
conda config --add channels https://conda.anaconda.org/conda-forge/noarch
conda config --add channels https://repo.continuum.io/pkgs/main/linux-64
conda config --add channels https://repo.continuum.io/pkgs/main/noarch
conda config --add channels https://repo.continuum.io/pkgs/free/linux-64
conda config --add channels https://repo.continuum.io/pkgs/free/noarch
conda config --add channels https://repo.continuum.io/pkgs/r/linux-64
conda config --add channels https://repo.continuum.io/pkgs/r/noarch
conda config --add channels https://repo.continuum.io/pkgs/pro/linux-64
conda config --add channels https://repo.continuum.io/pkgs/pro/noarch
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/linux-64
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/noarch

#添加中国源
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/

Rstudio

系统的Rstudio调用conda的R的话，需要修改配置文件
/etc/rstudio/rserver.conf

没有权限的话，用conda 安装R包，然后加入到lib里面
vim ~/.Rprofile

options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")
mylib=.libPaths()
mylib=c(mylib,"/public/home/nong/miniconda3/lib/R/library")
.libPaths(mylib)
rm(mylib)

R 包安装

Bioconductor 在R包前面加bioconductor ,不区分大小写

conda install bioconductor-clusterprofiler
conda install bioconductor-clusterprofiler
conda install bioconductor-org.Hs.eg.db bioconductor-org.Mm.eg.db bioconductor-org.Dr.eg.db
conda install bioconductor-pathview

运行的R版本

rsession-which-r=/home/nong/miniconda2/bin/R

R运行的依赖，以及R Packages的安装位置

rsession-ld-library-path=/home/nong/miniconda2/lib:/home/nong/miniconda2/lib/R/library

http://docs.rstudio.com/ide/server-pro/r-sessions.html

## 创建新环境

conda create -n circseq_cup python=2.7
conda activate circseq_cup

退出环境

source deactivate circseq_cup

#下载
conda install -y picard bowtie bowtie2 hisat2 blast  trinity
conda install -y  samtools tophat cap3 STAR
conda install -y bedtools pysam docopt biopython 
conda install -y  fastqc multiqc 
conda install perl-perlio-gzip perl-db-file