bahlolab/nf-MPS-gatk-bp:v1.3.1

$ singularity pull shub://bahlolab/nf-MPS-gatk-bp:v1.3.1

Singularity Recipe

Bootstrap:docker
From: continuumio/miniconda3:latest

%labels
  AUTHOR Jacob Munro
  AUTHOR bahlolab

%post
    alias conda="/opt/conda/bin/conda"
    conda config --add channels conda-forge
    conda config --add channels bioconda
    conda config --add channels r
    conda install -y \
        gatk4=4.0.12.0 \
        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
    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/gatk4-4.0.12.0-0/gatk-package-4.0.12.0-local.jar

Collection


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key value
id /containers/bahlolab-nf-MPS-gatk-bp-v1.3.1
collection name bahlolab/nf-MPS-gatk-bp
branch master
tag v1.3.1
commit 305bc71c78ef2ff7df55ebdf612fad02e934d8b7
version (container hash) d61d756c0496b5b184cff6ba7172b865
build date 2019-01-21T15:26:38.557Z
size (MB) 3291
size (bytes) 1286311967
SIF Download URL (please use pull with shub://)
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