1. 下载基于ARACNe-AP软件:https://github.com/califano-lab/ARACNe-AP
mkdir ARACNe-AP
git clone https://github.com/califano-lab/ARACNe-AP.git
2. 下载java:https://www.oracle.com/java/technologies/downloads/#java8
mkdir JAVA_JDK
tar -zxvf /your/pathway/to/jdk-8u131-linux-x64.tar.gz
3. 下载ANTs:https://ant.apache.org/bindownload.cgi
mkdir ANTs
tar -zxvf /your/pathway/to/apache-ant-1.9.14-bin.tar.gz
4. 配置环境变量
vim ~/.bashrc
#写入以下内容
export JAVA_HOME=/YOUR/PATHWAY/TO/jdk1.8.0_211
export CLASSPATH=$:CLASSPATH:$JAVA_HOME/lib/
export PATH=$PATH:$JAVA_HOME/bin
export ANT_HOME=/YOUR/PATHWAY/TO/apache-ant-1.9.15/
export PATH=$ANT_HOME/bin:$PATH
验证是否安装成功
source ~/.bashrc
java -version
ant -version
5. 构建JAVA需要的aracne.jar文件
cd ARACNe-AP
ant main #会产生dist/aracne.jar文件
6. 运行ARACNe-AP
6.1 准备输入文件:
(1)表达谱文件
(2)TF文件
6.2 运行软件
#Step1 Calculate threshold with a fixed seed
java -Xmx5G -jar ARACNe-AP/dist/aracne.jar -e RNAseq/exp.txt -o ARACNe --tfs TF.txt --pvalue 1E-8 --seed 1 --calculateThreshold
#Step1: Run 100 reproducible bootstraps
for i in {1..100}
do
java -Xmx5G -jar ARACNe-AP/dist/aracne.jar -e RNAseq/exp.txt -o ARACNe --tfs TF.txt --pvalue 1E-8 --seed $i --threads 60
done
#Step3: Consolidate bootstraps in the output folder
java -Xmx5G -jar ARACNe-AP/dist/aracne.jar -o ARACNe --consolidate --threads 60