Singularity

# Copyright 2020 [LIPM]
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at

# http://www.apache.org/licenses/LICENSE-2.0

# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
#    limitations under the License.

Bootstrap: docker
From: debian:sid-slim

%files

source/E2P2v4-20221206.tar /opt/

%runscript
	exec /usr/local/bin/E2P2 "$@"

%help

Usage: singularity exec $CONTAINER run_pipeline.py

This is an E2P2 container built upon
 - E2P2 20221206 master version https://github.com/carnegie/E2P2
 - Priam (last java version) (included in E2P2 tarball)
 - ncbi-blast-2.12.0+
 - python 3


%labels
    Maintainer Ludovic.Cottret@inrae.fr & Sebastien.Carrere@inrae.fr
    E2P2 : https://github.com/carnegie/E2P2
    
%post

	apt update && \
    apt install -y \
		procps wget \
        openjdk-8-jre   \
        python3         \
        git
   

	mkdir -p /opt
	cd /opt

    # E2P2 pipeline
    mkdir -p /usr/local/bin
    tar xf E2P2v4-20221206.tar && rm E2P2v4-20221206.tar
    echo '#!/bin/bash\n\npython3 /opt/E2P2/pipeline/run_pipeline.py -b /opt/ncbi-blast-2.12.0+/bin/blastp -bb /opt/ncbi-blast-2.12.0+/bin/ -j java -ps /opt/PRIAM/PRIAM_search.jar -r /opt/data/E2P2/blastdb/rpsd-4.2.fasta -pp /opt/data/E2P2/profiles $@'  >> /usr/local/bin/E2P2 && chmod +x /usr/local/bin/E2P2
	
    # blast+ binaries
	wget -O /opt/ncbi-blast-2.12.0+-x64-linux.tar.gz ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-x64-linux.tar.gz
    tar xvf ncbi-blast-2.12.0+-x64-linux.tar.gz 
    rm -f /opt/ncbi-blast-2.12.0+-x64-linux.tar.gz

    # E2P2 data
    mkdir -p /opt/data/E2P2
    cd /opt/data/E2P2
    wget https://ftp.dpb.carnegiescience.edu/rpsd/release_2019-03-07/blastdb.tar.gz
    wget https://ftp.dpb.carnegiescience.edu/rpsd/release_2019-03-07/profiles.tar.gz
    wget https://ftp.dpb.carnegiescience.edu/rpsd/release_2019-03-07/maps.tar.gz
    wget https://ftp.dpb.carnegiescience.edu/rpsd/release_2019-03-07/weights.tar.gz
    
    tar zxvf blastdb.tar.gz
    tar zxvf profiles.tar.gz
    tar zxvf maps.tar.gz
    tar zxvf weights.tar.gz

    rm -f *.tar.gz

    rm -rf /opt/E2P2/data/*

    mv maps weights /opt/E2P2/data
    
    # PRIAM program
    mkdir -p /opt/PRIAM
    cd /opt/PRIAM
    mv /opt/E2P2/PRIAM_search.jar .
    
    mkdir /opt/run

    chmod -R 755 /opt/run
    apt clean && apt autoremove && apt purge 


%environment
export LC_ALL=C
export HOME=/opt/run
export PATH=/opt/E2P2/pipeline:$PATH
cd $HOME