kingzhuky/meripseqpipe:latest

$ singularity pull shub://kingzhuky/meripseqpipe:latest

Singularity Recipe

Bootstrap: docker
From: nfcore/base:1.7
%files
environment.yml /
%labels
authors="Kaiyu Zhu, Yu Sun" 
description="Docker image containing all requirements for nf-core/meripseqpipe pipeline"
%post

conda env create -f /environment.yml && conda clean -a
PATH=/opt/conda/bin:$PATH
PATH=/opt/conda/envs/nf-core-meripseqpipe-1.0dev/bin:$PATH
PATH=/mspc:$PATH

# install MATK
wget http://matk.renlab.org/download/MATK-1.0.jar

# install QNB
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

# install MeTDiff
git clone https://github.com/compgenomics/MeTDiff.git && \
R CMD build MeTDiff/ && \
R CMD INSTALL MeTDiff_1.0.tar.gz && \
rm -rf MeTDiff*

# install MeTPeak
git clone https://github.com/compgenomics/MeTPeak.git && \
R CMD build MeTPeak/ && \
R CMD INSTALL MeTPeak_1.0.0.tar.gz && \
rm -rf MeTPeak*

# install MSPC
conda install -y unzip
wget -O mspc.zip "https://github.com/Genometric/MSPC/releases/download/v4.0.0/linux-x64.zip" && \
unzip mspc.zip -d mspc && \
chmod 775 mspc/mspc && \
rm mspc.zip
%environment
export PATH=/opt/conda/bin:$PATH
export PATH=/opt/conda/envs/nf-core-meripseqpipe-1.0dev/bin:$PATH
export PATH=/mspc:$PATH
%runscript
exec /bin/bash "$@"
%startscript
exec /bin/bash "$@"

Collection

• Name: kingzhuky/meripseqpipe
• License: MIT License

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