diff --git a/snakePipes.def b/snakePipes.def new file mode 100644 index 0000000000000000000000000000000000000000..cf400835d47bad9fa1ceee4aacd9ff4f504b60ed --- /dev/null +++ b/snakePipes.def @@ -0,0 +1,59 @@ +BootStrap: docker +From: ubuntu:22.04 +Stage: build + +%help +This is a singularity container packing the snakePipes pipeline in version 2.5.3 and all the dedicated environnement set up for proper usage of the pipeline +Author : marine.bergot@u-bourgogne.fr +Bionano Solve pipeline is the property of Bionano Genomics Inc. All Rights Reserved + +Launching a complete assembly could be perform with this command : + +singularity exec -e snakePipes.sif \ +hicexplorer command + +exemple : + +singularity exec -e snakePipes.sif HiC --help + + +%environment + +DEBIAN_FRONTEND=noninteractive + + +%post + +apt-get update && apt-get -y upgrade +apt-get -y install build-essential wget bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 git +apt-get clean + + +# install python3.9 +apt-get -y install python3.9 +apt-get -y install build-essential zlib1g-dev libncurses5-dev libgdbm-dev libnss3-dev libssl-dev libreadline-dev libffi-dev wget + + +#Installing Miniconda 3 +wget -c https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh +bash Miniconda3-py39_4.12.0-Linux-x86_64.sh -bfp /usr/local +#Conda configuration of channels from .condarc file +conda config --file /.condarc --add channels defaults +conda config --file /.condarc --add channels conda-forge +conda update conda +#List installed environments +conda list + + + +conda install -c mpi-ie -c bioconda -c conda-forge snakePipes + + +%labels +Maintainer Marine Bergot +Updater Marine Bergot <marine.bergot@u-bourgogne.fr> +ContainerVersion v0.1 +snakePipes pipeline v2.5.3 + +%runscript +echo "OK"