# vep # 使用vep對manta結果進行注釋 # manta結果是染色體結構變異(SV),這里使用vep進行注釋 # vep官方說明文檔： # http://asia.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html # 安裝 conda create -n VEP conda activate VEP conda install -c bioconda ensembl-vep # 報錯: # Elapsed: # An HTTP error occurred when trying to retrieve this URL. # HTTP errors are often intermittent, and a simple retry will get you on your way. # 查詢發現是清華鏡像的問題，怒換中科大鏡像 # 嘗試：顯示現在的鏡像： conda config --show - https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/linux-64 - https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/ - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/ - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/ - https://mirrors.ustc.edu.cn/anaconda/pkgs/free/ # 刪除清華鏡像，只留下中科大的： conda config --remove channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/ conda config --remove channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/ # 再次安裝，繼續報錯 conda install -c bioconda ensembl-vep # Collecting package metadata (current_repodata.json): done # Solving environment: failed with initial frozen solve. Retrying with flexible solve. # Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. # Collecting package metadata (repodata.json): done # Solving environment: failed with initial frozen solve. Retrying with flexible solve. # Solving environment: - # Found conflicts! Looking for incompatible packages. failed # UnsatisfiableError: # 更新conda conda update -n base conda conda update -all # 修改頻道 conda config --add channels conda-forge conda config --set channel_priority flexible # 安裝成功！