aghozlane/entvirus:latest

$ singularity pull shub://aghozlane/entvirus:latest

Singularity Recipe

BootStrap: docker
From: ubuntu:16.04
%help
Entvirus workflow

%environment
    export LC_ALL=C

%files
    ./bin/*.py /usr/local/bin

%post
    apt -y update && apt -y install python-pip gcc g++ wget unzip gcj-jdk python3-pip git pigz
    # Bowtie2
    wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.4.1/bowtie2-2.3.4.1-linux-x86_64.zip
    unzip bowtie2-2.3.4.1-linux-x86_64.zip
    mv bowtie2-2.3.4.1-linux-x86_64/bowtie2* /usr/local/bin/
    rm -rf bowtie2-2.3.4.1-linux-x86_64.zip bowtie2-2.3.4.1-linux-x86_64
    # Alientrimmer
    wget ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/AlienTrimmer_0.4.0.tar.gz
    tar -zxf AlienTrimmer_0.4.0.tar.gz
    cd AlienTrimmer_0.4.0/src && sed "s:-march=native::g" -i Makefile && make && mv AlienTrimmer /usr/local/bin/ && cd
    # Khmer
    pip2 install khmer
    # Megahit
    wget https://github.com/voutcn/megahit/releases/download/v1.1.3/megahit_v1.1.3_LINUX_CPUONLY_x86_64-bin.tar.gz
    tar -zxf megahit_v1.1.3_LINUX_CPUONLY_x86_64-bin.tar.gz
    mv megahit_v1.1.3_LINUX_CPUONLY_x86_64-bin/megahit* /usr/local/bin/
    rm -rf megahit_v1.1.3_LINUX_CPUONLY_x86_64-bin megahit_v1.1.3_LINUX_CPUONLY_x86_64-bin.tar.gz
    # Spades
    wget http://cab.spbu.ru/files/release3.12.0/SPAdes-3.12.0-Linux.tar.gz
    tar -zxf SPAdes-3.12.0-Linux.tar.gz
    mv SPAdes-3.12.0-Linux/bin/* /usr/local/bin/
    # pysam pandas
    pip install pysam pandas
    # taxadb
    pip3 install taxadb
    # blast
    wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz
    tar -zxf ncbi-blast-2.7.1+-x64-linux.tar.gz
    mv ncbi-blast-2.7.1+/bin/* /usr/local/bin/
    rm -rf ncbi-blast-2.7.1+-x64-linux.tar.gz ncbi-blast-2.7.1+/
    # BMGE
    wget ftp://ftp.pasteur.fr/pub/gensoft/projects/BMGE/BMGE-1.12.tar.gz
    tar -zxf BMGE-1.12.tar.gz
    mv BMGE-1.12/BMGE.jar /usr/local/bin/
    # gotree
    wget https://github.com/fredericlemoine/gotree/releases/download/v0.2.10/gotree_amd64_linux
    mv gotree_amd64_linux /usr/local/bin/gotree
    # iqtree
    wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.6/iqtree-1.6.6-Linux.tar.gz
    tar -zxf iqtree-1.6.6-Linux.tar.gz
    mv iqtree-1.6.6-Linux/bin/* /usr/local/bin/
    # mafft
    wget https://mafft.cbrc.jp/alignment/software/mafft-7.402-linux.tgz
    tar -zxf mafft-7.402-linux.tgz
    mv mafft-linux64/mafftdir/bin/* /usr/local/bin/
    # MBMA
    #git clone https://gitlab.pasteur.fr/aghozlan/mbma_singularity.git
    #mv mbma_singularity/* /usr/local/bin/
    # clean
    rm -rf .cache/
    # execute python
    chmod +x /usr/local/bin/*.py
    # pasteur dir
    mkdir -p /pasteur /local

Collection

• Name: aghozlane/entvirus
• License: None

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