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QuaCK_singularity_recipe_file.txt
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QuaCK_singularity_recipe_file.txt
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Bootstrap: debootstrap
OSVersion: xenial
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
Include: apt
%help
This container is built to run the QuaCK repo located on github: https://github.com/tbrunetti/QuaCK
%setup
cp run_GWAS_QC_filtering_pipeline.py $SINGULARITY_ROOTFS
cp run_GWAS_QC_filtering_pipeline.py.json $SINGULARITY_ROOTFS
cp run_GWAS_QC_filtering_pipeline.json $SINGULARITY_ROOTFS
echo $SINGULARITY_ROOTFS
ls $SINGULARITY_ROOTFS
%files
LICENSE
format_sample_sheet_names.py /mnt
generate_illumina_snp_stats.py /mnt
generate_report.py /mnt
hapmap_trio_info.txt /mnt
Parameter_Definitions.pdf /mnt
pre-QC-initialization-workflow.pdf /mnt
pre-QC-initialization-workflow.png /mnt
QC-pipeline-workflow.pdf /mnt
QC-pipeline-workflow.png /mnt
run_GWAS_QC_filtering_pipeline.py /mnt
transparent_AMC_cropped.png /mnt
new_TGP_vol1_MEGA_flipped_triallelic_removed_no_atgc.bed /mnt
new_TGP_vol1_MEGA_flipped_triallelic_removed_no_atgc.bim /mnt
new_TGP_vol1_MEGA_flipped_triallelic_removed_no_atgc.fam /mnt
run_GWAS_QC_filtering_pipeline.py.json /mnt
run_GWAS_QC_filtering_pipeline.json /mnt
plink /mnt
%runscript
echo "chunkypipes framework is ready!"
cd /mnt
exec /usr/local/bin/chunky "$@"
%post
echo "Installing all container dependencies!"
apt-get -y update
apt-get -y install software-properties-common
apt-add-repository universe
apt-get -y update
apt-get -y install python
apt-get -y install python-pip
echo "verifiying pip install"
pip -V
pip install chunkypipes
pip install pandas
pip install numpy
pip install matplotlib==2.2.4
pip install fpdf
pip install Pillow
pip install pypdf2
pip install statistics
pip install xlrd
pip install scipy==1.2.0
pip install seaborn==0.8.0
/usr/local/bin/chunky init /mnt
cp run_GWAS_QC_filtering_pipeline.py /mnt/.chunky/pipelines
cp run_GWAS_QC_filtering_pipeline.py.json /mnt/.chunky/configs
cp run_GWAS_QC_filtering_pipeline.py /mnt/.chunky/pipelines/run_GWAS_QC_filtering_pipeline
cp run_GWAS_QC_filtering_pipeline.json /mnt/.chunky/configs
cd /mnt
ls
chmod -R a+rwx /mnt
chmod -R a+rwx /mnt/.chunky
%environment
CHUNKY_HOME=/mnt
export CHUNKY_HOME
export PATH="${PATH}:/mnt:/usr/bin:/bin:/usr/local/sbin/:/usr/local/bin"
export PYTHONPATH="${PYTHONPATH}:/mnt"
export PYTHONPATH="${PYTHONPATH}:/usr/local/bin/:/usr/lib/python2.7/:/usr/bin/"