aspera

  1. mkdir app && cd app
  2. wget http://download.asperasoft.com/download/sw/connect/3.7.4/aspera-connect-3.7.4.147727-linux-64.tar.gz &
  3. tar zxvf aspera-connect-3.7.4.147727-linux-64.tar.gz
  4. bash aspera-connect-3.7.4.147727-linux-64.sh #安装
  5. cd ~ # 去根目录
  6. ls -alh # 如果看到.aspera文件夹，代表安装成功
  7. echo 'export PATH=~/.aspera/connect/bin:$PATH' >> ~/.bashrc
  8. source ~/.bashrc
  9. ascp --help  #ok

conda安装


fastqc multiqc samtools htslib bcftools trimmomatic bwa gatk

  1. conda install -c bioconda fastqc multiqc trimmomatic htslib bcftools bwa gatk4
  2. conda install -c bioconda samtools=1.9


troubleshooting

  1. 运行samtools报错是因为版本太低 强制安装1.9版本可以解决问题

samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

MAC

Julia 设置RCall和PyCall

  1. Sys.getenv("R_HOME") #在R中获取地址
  2. using Pkg
  3. Pkg.add("RCall")
  4. ENV["R_HOME"] = "/Library/Frameworks/R.framework/Resources"
  6. conda activate julia #shell
  7. which python #shell
  8. Pkg.add("PyCall")
  9. ENV["PYTHON"] = "/Users/Saul/miniconda3/envs/julia/bin/python"
  10. Pkg.build("PyCall")
  11. pip install xlrd==1.2.0