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
- Name: chrarnold/Singularity_images
- License: GNU General Public License v3.0
View on Datalad
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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