BootStrap: library
From: ubuntu:16.04


%help
	

This container launches the OMM_MACSE pipeline used to buid the OrthoMaM Database (V10).
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    usage (basic): OMM_MACSE_v10.01.sif --out_dir out_dir --out_file_prefix out_file_prefix --in_seq_file nucleotide_coding_sequences_to_align.fasta
    usage (help) : OMM_MACSE_v10.01.sif

    usage (example): OMM_MACSE_v10.01.sif --in_seq_file LOC_48720.fasta --out_dir RES_LOC_48720 --out_file_prefix LOC_48720 

For more details please see the pipeline documentation pages on the MACSE website:
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https://bioweb.supagro.inra.fr/macse


If you use this pipeline please cite:
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OrthoMam v10 (the paper describing this pipeline)
    Celine Scornavacca, Khalid Belkhir, Jimmy Lopez, Rémy Dernat, Frédéric Delsuc, Emmanuel J P Douzery, Vincent Ranwez, OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes, Molecular Biology and Evolution, Volume 36, Issue 4, April 2019, Pages 861–862, https://doi.org/10.1093/molbev/msz015

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MACSE V2.03 (extensively used in this pipeline)
    Vincent Ranwez, Emmanuel J P Douzery, Cédric Cambon, Nathalie Chantret, Frédéric Delsuc, MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons, Molecular Biology and Evolution, Volume 35, Issue 10, October 2018, Pages 2582–2584, https://doi.org/10.1093/molbev/msy159

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MAFFT v7.271 (default) or MUSCLE v3.8.31 (depending on selected options)
    Katoh K., Standley D.M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution, 30(4), 772-780. Edgar R.C. (2004). 
    MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 32(5), 1792-1797.

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HMMCleaner V1_8_VR2 (default)
    Di Franco, Arnaud, et al. Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences. BMC Evolutionary Biology, vol. 19, no. 1, 2019. Gale Academic Onefile, Accessed 13 Oct. 2019.
        
    Note that this script used a modified version (V1_8_VR2) of HMMCleaner V1_8 developped by Raphael Poujol
        Vincent Ranwez modified the original perl script so that
            1. sequences and sequence names are unchanged even when they contain unusual characters
            2. all output files are saved in the current directory (rather that being spread in the directory containing the input fasta file and HMMCleaner perl script)
    
            HMMCleaner has since been re-written by Arnaud Di Franco and a more recent release of HMMCleaner is available here: https://metacpan.org/pod/HmmCleaner.pl

%post
    apt-get -y update 
    apt-get -y install unzip
    apt-get -y install wget
    apt-get -y install openjdk-8-jre
    apt-get -y install hmmer=3.1b2-2
    apt-get -y install muscle=1:3.8.31+dfsg-1
    apt-get -y install mafft=7.271-1

    apt list muscle mafft
    rm -rf /var/lib/apt/lists/*
    
    wget https://bioweb.supagro.inra.fr/macse/releases/OMM_MACSE_V10.01.zip
    unzip OMM_MACSE_V10.01.zip
    chmod 755 /OMM_MACSE_V10.01/*.sh
    chmod 755 /OMM_MACSE_V10.01/*/*.sh
    


%environment
    export LC_ALL=C
    export LG_HOME_PATH="/OMM_MACSE_V10.01/"
    export LG_MAFFT="mafft"
    export LG_MUSCLE="muscle"
    export LG_MACSE="/OMM_MACSE_V10.01/macse_v2.03.jar"
    export LG_HMMCLEANER="/OMM_MACSE_V10.01/HMMcleanerV1_8_VR2/HMMcleanAA_VR.pl "

    

%runscript
    exec bash /OMM_MACSE_V10.01/S_OMM_MACSE_V10.01.sh "$@"

%files
    #OMM_MACSE_V10.01.zip

%labels
    Author Vincent Ranwez

#sudo singularity  build OMM_MACSE_V10.01.sif OMM_MACSE_V10.01_sing.def
#singularity run OMM_MACSE_V10.01.sif
#singularity run-help OMM_MACSE_V10.01.sif