monaghaa/rnaseq:latest

$ singularity pull shub://monaghaa/rnaseq:latest

Singularity Recipe

BootStrap: docker
From: ubuntu:16.04

##################################
#notes from andy:

#I didn't check to see if any genomics databases were needed
#these can generally be installed outside the container
#but sometimes they need environment variables to be set 
##################################

%post

    # install some system deps
    apt-get -y update
    apt-get -y install locales curl bzip2 less unzip git wget vim ant default-jdk
    # this is a X11 dep
    apt-get -y install libxext6
    # tools to open PDF and HTML files
    apt-get -y install firefox xpdf
    # some extra devel libs
    apt-get -y install zlib1g-dev libssl-dev libpng-dev uuid-dev
    # other
    locale-gen en_US.UTF-8
    apt-get clean

    # download and install miniconda3
    curl -sSL -O https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
    bash Miniconda3-latest-Linux-x86_64.sh -p /opt/miniconda3 -b
    rm -fr Miniconda3-latest-Linux-x86_64.sh
    export PATH=/opt/miniconda3/bin:$PATH
    conda update -n base conda
    conda config --add channels conda-forge
    conda config --add channels bioconda

    # install some dependencies to build R packages
    apt-get -y install build-essential gfortran

    # install some bioinfo tools from Bioconda
    conda install -y -c bioconda cutadapt fastqc hisat2 samtools rsem bowtie2
    

%environment
    export LANG=en_US.UTF-8
    export LANGUAGE=en_US:en
    export LC_ALL=en_US.UTF-8
    export XDG_RUNTIME_DIR=""
    export PATH=/opt/miniconda3/bin:$PATH

Collection

• Name: monaghaa/rnaseq
• License: None

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