nealplatt/sH_hybridization:latest

$ singularity pull shub://nealplatt/sH_hybridization:latest

Singularity Recipe

BootStrap: docker
From: ubuntu:16.04

%labels
AUTHOR Roy "Neal" Platt
MAINTAINER rplatt@txbiomed.org
VERSION 0.1
DATE 5 Feb 2018

%post
    apt-get update
    apt-get clean
    apt-get install -qy \
                wget \
		bzip2 \
                r-base \
                r-base-dev \
                default-jre \
                bwa \
                samtools \
                git \
                zip \
		nano \
		vim \
                dialog

    mkdir /usr/software

    cd /usr/software/
    
    #Install bioconda
    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
    chmod u+x Miniconda3-latest-Linux-x86_64.sh 
    bash ./Miniconda3-latest-Linux-x86_64.sh -b -p /usr/software/miniconda3
    export PATH="/usr/software/miniconda3/bin:$PATH"
    conda install -y -c bioconda snakemake
    rm Miniconda3-latest-Linux-x86_64.sh
    ln -s /usr/software/miniconda3/bin/* /usr/local/bin/

    #Install GATK
    wget https://github.com/broadinstitute/gatk/releases/download/4.0.1.1/gatk-4.0.1.1.zip
    unzip gatk-4.0.1.1.zip
    rm gatk-4.0.1.1.zip
    ln -s /usr/software/gatk-4.0.1.1/gatk /usr/local/bin/

    wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
    unzip Trimmomatic-0.36.zip
    ln -s /usr/software/Trimmomatic-0.36/trimmomatic-0.36.jar /usr/software/
    rm -r Trimmomatic-0.36.zip Trimmomatic-0.36



#%runscript
#    exec /bin/bash

Collection


View on Datalad

Metrics

key value
id /containers/nealplatt-sH_hybridization-latest
collection name nealplatt/sH_hybridization
branch master
tag latest
commit 83fcebaa5cbc92da7581aaca36ead0358ed4f660
version (container hash) a16cb090803aab238c9c11d5866f6147
build date 2018-02-06T23:37:02.039Z
size (MB) 2595
size (bytes) 1360052255
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
We cannot guarantee that all containers will still exist on GitHub.