Merge branch 'master' of gitlab.gad-bioinfo.org:gad-public/singularity

hicexplorer.def

+BootStrap: docker
+From: ubuntu:22.04
+Stage: build
+
+%help
+This is a singularity container packing the Hicexplorer pipeline in version 3.7.2 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 hicexplorer_3.7.2.sif \
+hicexplorer command
+
+exemple : 
+
+singularity exec -e -w bionano_solve_3.7.sif hicBuildMatrix --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 hicexplorer -c bioconda -c conda-forge
+
+
+%labels
+Maintainer Marine Bergot
+Updater Marine Bergot <marine.bergot@u-bourgogne.fr>
+ContainerVersion v0.1
+Hicexplorer pipeline v3.7.2
+
+%runscript
+echo "OK"

snakePipes.def

+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"