MetaboIGNITER/container-metfrag-cli-batch:latest

$ singularity pull shub://MetaboIGNITER/container-metfrag-cli-batch:latest

Singularity Recipe

Bootstrap: docker
From: quay.io/biocontainers/metfrag:2.4.5--1
%files
runTest1.sh /usr/local/bin/runTest1.sh
metfrag.sh /usr/local/bin/metfrag.sh
run_metfrag.sh /usr/local/bin/run_metfrag.sh
%labels
software.version=2.4.5
version=0.9
software=metfrag-cli-batch
MAINTAINER PhenoMeNal-H2020 Project ( phenomenal-h2020-users@googlegroups.com )
Description="MetFrag command line interface for batch processing."
%post
#FROM ubuntu:16.04




# Update & upgrade sources
#RUN apt-get -y update

# Install development files needed
#RUN apt-get -y install wget openjdk-8-jdk-headless parallel zip 

# Clean up
#RUN apt-get -y clean && apt-get -y autoremove && rm -rf /var/lib/{cache,log}/ /tmp/* /var/tmp/*

# Install MetFrag
#RUN wget -O /usr/local/bin/MetFragCLI.jar http://msbi.ipb-halle.de/~cruttkie/92f73acb731145c73ffa3dfb8fd59581bee0d844963889338c3ec173874b5a5f/MetFrag-2.4.3.jar

wget http://central.maven.org/maven2/net/sf/jni-inchi/jni-inchi/0.8/jni-inchi-0.8.jar && mkdir -p /root/.jnati/repo/ && jar xf jni-inchi-0.8.jar && mv META-INF/jniinchi /root/.jnati/repo/

# Add testing to container
chmod +x /usr/local/bin/runTest1.sh

# Add metfrag.sh
chmod +x /usr/local/bin/metfrag.sh

# Add run_metfrag.sh
chmod +x /usr/local/bin/run_metfrag.sh

# Define Entry point script

%runscript
exec metfrag "$@"
%startscript
exec metfrag "$@"

Collection

• Name: MetaboIGNITER/container-metfrag-cli-batch
• License: None

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