yaesoubilab/containers:latest
$ singularity pull shub://yaesoubilab/containers:latest
Singularity Recipe
Bootstrap: docker
From: ubuntu:18.04
%setup
# mkdir ${SINGULARITY_ROOTFS}/repos
# mkdir ${SINGULARITY_ROOTFS}/repos/StatisticalDistributionsLib
# mkdir ${SINGULARITY_ROOTFS}/repos/SimulationLib
# mkdir ${SINGULARITY_ROOTFS}/repos/TBABM
mkdir ${SINGULARITY_ROOTFS}/params_bucket
%files
%environment
%post
apt-get update
apt-get -y install cmake make git libeigen3-dev libboost-all-dev clang python-pip
pip install csvkit
export CC=/usr/bin/clang
export CXX=/usr/bin/clang++
git clone https://github.com/yaesoubilab/StatisticalDistributionsLib repos/StatisticalDistributionsLib/
git clone https://github.com/yaesoubilab/SimulationLib repos/SimulationLib/
git clone https://github.com/yaesoubilab/TBABM repos/TBABM/
cd repos/StatisticalDistributionsLib && cmake . && make install && cd ..
cd SimulationLib/SimulationLib && cmake . && make install && cd ../..
cd TBABM && git checkout new-tb-initialization && cmake . && make && cd ../..
NOW=`date`
echo "export NOW=\"${NOW}\"" >> $SINGULARITY_ENVIRONMENT
# With this post section, it should be possible to simply cp the TBABM
# directory over, go to params/ and run ./updateJSONs.sh, and then run
# the simulation as normal
%runscript
echo "Container was created $NOW"
echo "Arguments received: $*"
# exec cd ${SINGULARITY_ROOTFS}/repos/TBABM/src && ./TBABM "$@"
%startscript
nc -lp $LISTEN_PORT
%test
grep -q NAME=\"Ubuntu\" /etc/os-release
if [ $? -eq 0 ]; then
echo "Container base is Ubuntu as expected."
else
echo "Container base is not Ubuntu."
fi
%labels
Author marcus.russi@yale.edu
Version v0.0.1
URL https://github.com/yaesoubilab
%help
This is a production container used for cluster-based runs of TBABM
Collection
- Name: yaesoubilab/containers
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/yaesoubilab-containers-latest |
collection name | yaesoubilab/containers |
branch | master |
tag | latest |
commit | 611ad111d2d98d5ad53d024133dcd8151112e33c |
version (container hash) | 2223f5a3691f0cd147a4d951676c0e84 |
build date | 2019-04-23T20:55:38.011Z |
size (MB) | 1495 |
size (bytes) | 481300511 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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