背景:Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states 。(官网下载需填邮箱)
网址:http://software.broadinstitute.org/gsea/index.jsp
遇到问题: (集中在Java版本)1. GSEA运行需要Java; 2. 电脑自带Java,打不开GSEA
发现问题: GSEA支持java 版本(java 8)与电脑Java版本(java 11.0.1)不匹配。(在下载的时候有提示java版本,没看说明导致!!!)
解决问题:
1. ##查看电脑 java 版本
java -version
2.我选择用conda安装java 8
## 根据你自己的电脑来选择性安装conda
wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
# 然后修改镜像,加快下载速度
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
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
conda config --set show_channel_urls yes
##安装
sh Miniconda3-latest-Linux-x86_64.sh
## 把java8安装到指定环境,隔离开来
conda create -n qc
source activate qc
conda install openjdk=8.0.152
##版本成功,查看java版本
java -version
##运行:
java -jar gsea-3.0.jar
##很多broad institute出品的软件都依赖于 java8
## 想了解版本,
conda search openjdk
Loading channels: done
# Name Version Build Channel
openjdk 7.0.161 zulu7.21.0.3_0 anaconda/cloud/conda-forge
openjdk 8.0.112 zulu8.19.0.1_0 anaconda/cloud/conda-forge
openjdk 8.0.112 zulu8.19.0.1_1 anaconda/cloud/conda-forge
openjdk 8.0.112 zulu8.19.0.1_2 anaconda/cloud/conda-forge
openjdk 8.0.112 zulu8.19.0.1_3 anaconda/cloud/conda-forge
openjdk 8.0.121 0 pkgs/free
openjdk 8.0.121 1 pkgs/free
openjdk 8.0.121 zulu8.20.0.5_0 anaconda/cloud/conda-forge
openjdk 8.0.144 zulu8.23.0.3_0 anaconda/cloud/conda-forge
openjdk 8.0.144 zulu8.23.0.3_1 anaconda/cloud/conda-forge
openjdk 8.0.144 zulu8.23.0.3_2 anaconda/cloud/conda-forge
openjdk 8.0.152 h393ad39_1 pkgs/main
openjdk 8.0.152 he2ab291_0 pkgs/main
openjdk 8.0.192 h470a237_2 anaconda/cloud/conda-forge
openjdk 9.0.7 h470a237_14 anaconda/cloud/conda-forge
openjdk 9.0.7 h470a237_15 anaconda/cloud/conda-forge
openjdk 9.0.7 h470a237_2 anaconda/cloud/conda-forge
openjdk 9.0.7 h470a237_3 anaconda/cloud/conda-forge
openjdk 9.0.7 h470a237_4 anaconda/cloud/conda-forge
openjdk 9.0.7 zulu9.0.7.1_0 anaconda/cloud/conda-forge
openjdk 10.0.2 h470a237_14 anaconda/cloud/conda-forge
openjdk 10.0.2 h470a237_15 anaconda/cloud/conda-forge
openjdk 10.0.2 h470a237_2 anaconda/cloud/conda-forge
openjdk 10.0.2 h470a237_3 anaconda/cloud/conda-forge
openjdk 10.0.2 zulu10.3+5_0 anaconda/cloud/conda-forge
openjdk 11.0.1 h470a237_10 anaconda/cloud/conda-forge
openjdk 11.0.1 h470a237_11 anaconda/cloud/conda-forge
openjdk 11.0.1 h470a237_13 anaconda/cloud/conda-forge
openjdk 11.0.1 h470a237_14 anaconda/cloud/conda-forge
openjdk 11.0.1 h470a237_2 anaconda/cloud/conda-forge
openjdk 11.0.1 h470a237_3 anaconda/cloud/conda-forge
openjdk 11.0.1 zulu11.2.3_0 anaconda/cloud/conda-forge
感谢:Jimmy 以及生信技能树
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