JihedC/ChIP_seq_PE_Snakemake:latest

$ singularity pull shub://JihedC/ChIP_seq_PE_Snakemake:latest

Singularity Recipe

Bootstrap: docker
From: continuumio/miniconda3:4.7.12
%labels
AUTHOR jihed.chouaref@gmail.com

%environment
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# This sets global environment variables for anything run within the container export
PATH="/opt/conda/bin:/usr/local/bin:/usr/bin:/bin:"
unset CONDA_DEFAULT_ENV
export ANACONDA_HOME=/opt/conda

%post
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# This is going to be executed after the base container has been downloaded export
PATH=/opt/conda/bin:$PATH
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
#conda install --yes centrifuge=1.0.3
#conda install --yes krona=2.7.1
conda install --yes deeptools=3.5.0
#conda install --yes fastqc=0.11.9
#conda install --yes macs2=2.2.7.1
conda install --yes multiqc=1.9
conda install --yes picard=2.23.4
#conda install --yes r-base=3.6.1
conda install --yes cutadapt=2.10
conda install --yes trim-galore=0.6.6
conda install --yes bowtie2=2.4.1
conda install --yes samtools=1.10
conda install --yes snakemake=5.24.2
conda clean --index-cache --tarballs --packages --yes

Collection

• Name: JihedC/ChIP_seq_PE_Snakemake
• License: MIT License

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