chrarnold/Singularity_images:variant-calling_conda

$ singularity pull shub://chrarnold/Singularity_images:variant-calling_conda

Singularity Recipe

Bootstrap: docker
FROM: continuumio/miniconda3

%labels
  Version v1.0

%help
  Singularity image for the variant calling pipeline (Python 3)



%post

  # Add channels for Bioconda
  /opt/conda/bin/conda config --add channels defaults
  /opt/conda/bin/conda config --add channels bioconda
  /opt/conda/bin/conda config --add channels conda-forge

  # Install the tools
  /opt/conda/bin/conda install --yes bedtools samtools openssl=1.0 bwa fastqc trimmomatic cutadapt multiqc picard vcftools bcftools

  # wget --no-check-certificate -O gatk.tar.bz2 https://github.com/chrarnold/Singularity_images/raw/master/files/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2?raw=true

  # gatk-register gatk.tar.bz2

%environment

%test
   # bedtools --version
   # samtools --version
   # fastqc --version
   # bowtie2 --version
   # picard SortSam --version

Collection


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Metrics

key value
id /containers/chrarnold-Singularity_images-variant-calling_conda
collection name chrarnold/Singularity_images
branch master
tag variant-calling_conda
commit 5ca192fd291e6d79ff808f2eb04d240d8218e837
version (container hash) ac3bccee30ee3db3e0c327b08ea778b6
build date 2019-03-05T12:44:55.496Z
size (MB) 3122
size (bytes) 1552502815
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
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