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Installation
Kaiyu Zhu edited this page Dec 19, 2019
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Install Nextflow by using the following command:
curl -s https://get.nextflow.io | bash
git clone https://github.com/kingzhuky/m6APipe.git
Using the following command for buildind envrionment:
docker pull kingzhuky/m6apipe
Using the following command for buildind envrionment:
cd m6APipe && \
conda env create -f environment.yml && \
conda activate nf-core-m6APipe-1.0dev
Waiting for the conda environment of m6APipe to be built.
MATK is one of the PeakCalling tools which arranged by m6APipe. ( options )
wget http://matk.renlab.org/download/MATK-1.0.jar
MeTPeak is one of the PeakCalling tools which arranged by m6APipe. ( options )
git clone https://github.com/compgenomics/MeTPeak.git && \
R CMD INSTALL MeTPeak/ && \
rm -rf MeTPeak*
QNB is one of the methylation analysis methods which arranged by m6APipe. ( options )
wget https://cran.r-project.org/src/contrib/Archive/QNB/QNB_1.1.11.tar.gz && \
R CMD INSTALL QNB_1.1.11.tar.gz && \
rm QNB_1.1.11.tar.gz
MeTDiff is one of the methylation analysis methods which arranged by m6APipe. ( options )
git clone https://github.com/compgenomics/MeTDiff.git && \
R CMD INSTALL MeTDiff/ && \
rm -rf MeTDiff*
Download MSPC and Add it into enviroment variable $PATH
wget -O mspc.zip "https://github.com/Genometric/MSPC/releases/download/v4.0.0/linux-x64.zip" && \
unzip mspc.zip -d mspc
chmod +x mspc/mspc
echo "export PATH=`pwd`/mspc:\$PATH" >> ~/.bashrc
2018-2019 Center for Bioinformatics, Sun Yat-sen University Cancer Center