bahlolab/nf-MPS-gatk-bp:v1.3.2

$ singularity pull shub://bahlolab/nf-MPS-gatk-bp:v1.3.2

Singularity Recipe

Bootstrap:docker
From: continuumio/miniconda3:latest

%labels
  AUTHOR Jacob Munro
  AUTHOR bahlolab

%post
    alias conda="/opt/conda/bin/conda"
    conda update -n base -c defaults conda -y
    conda config --add channels conda-forge
    conda config --add channels bioconda
    conda config --add channels r
    conda install -y \
        gatk4=4.1.0.0 \
        bwa=0.7.17 \
        samtools=1.9 \
        bcftools=1.9 \
        r-base=3.5.1 \
        ensembl-vep=95 \
        multiqc=1.7 \
        fastp=0.19.5 \
        pysam=0.15.2 \
        openssl=1.0
    conda clean --all -y
    apt-get update && apt-get install -y procps
    sed 's:-Dsamjdk.compression_level=[0-9]:-Dsamjdk.compression_level=8:' -i /opt/conda/bin/gatk

%environment
    export PATH="/opt/conda/bin:/usr/local/bin:/usr/bin:/bin:"
    export GATK_LOCAL_JAR=/opt/conda/share/gatk4-4.1.0.0-0/gatk-package-4.1.0.0-local.jar

Collection


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Metrics

key value
id /containers/bahlolab-nf-MPS-gatk-bp-v1.3.2
collection name bahlolab/nf-MPS-gatk-bp
branch master
tag v1.3.2
commit 418fd02b1a9d83bc1a66870b3a11ad0e8c755ef0
version (container hash) f3a900a97acbf232f1f60f0608c00157
build date 2019-02-21T02:19:10.060Z
size (MB) 3309
size (bytes) 1294630943
SIF Download URL (please use pull with shub://)
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