lukegun/BIOMEC:def
$ singularity pull shub://lukegun/BIOMEC:def
Singularity Recipe
BootStrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%setup
mkdir -p ${SINGULARITY_ROOTFS}/runcode
cp -R BIOMEC/Analysiscode/. ${SINGULARITY_ROOTFS}/runcode/
cp BIOMEC/mecsim.cpython-37m-x86_64-linux-gnu.so ${SINGULARITY_ROOTFS}/runcode/mecsim.cpython-37m-x86_64-linux-gnu.so
%files
%runscript
# var 1 = Input file
if [ $# -ne 1 ];
then
echo "Please provide an Input file."
exit 1
fi
echo "running"
python3.7 ${SINGULARITY_ROOTFS}/runcode/PINTS_MECsim.py $1
echo "finished"
%labels
AUTHOR Luke Gundry
MECSim Aurthor: Gareth Kennedy
Currenly set up to run on python 3.7 in unbuntu bionic working in a singulrity Version 3.1 container hough higher should work
%post
# install packages and python modules
apt-get -y --force-yes install vim
apt-get -y --force-yes update
apt-get -y --force-yes install build-essential git
apt-get -y --force-yes install gfortran
apt-get -y --force-yes install python3.7
apt-get -y --force-yes install software-properties-common
apt-get -y --force-yes install bc
apt-add-repository universe
apt-get update
apt-get -y --force-yes install python3-pip python3.7-dev
python3.7 -m pip install --upgrade pip
python3.7 -m pip install pandas numpy scipy cma seaborn matplotlib
python3.7 -m pip install pints
# change permissions of files
chmod -R 777 ${SINGULARITY_ROOTFS}/runcode
Collection
- Name: lukegun/BIOMEC
- License: GNU General Public License v3.0
View on Datalad
Metrics
key | value |
---|---|
id | /containers/lukegun-BIOMEC-def |
collection name | lukegun/BIOMEC |
branch | main |
tag | def |
commit | 553fd7c675ffe440c3cf415d67a3b113697e6c4d |
version (container hash) | 29a78b42a0d276e679ab044424d0a6e24900470978c10c575c6a1e30c30acd07 |
build date | 2020-11-19T06:30:00.293Z |
size (MB) | 515.19140625 |
size (bytes) | 540217344 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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