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