jmhays/singularity-brer:latest
$ singularity pull shub://jmhays/singularity-brer:latest
Singularity Recipe
Bootstrap: docker
From: nvidia/cuda:8.0-devel-ubuntu16.04
%environment
# use bash as default shell
SHELL=/bin/bash
PATH=/usr/local/gromacs/bin:${PATH}
PYTHONPATH="/builds/sample_restraint/build/src/pythonmodule:\
/usr/local/lib/python3.5/dist-packages:/builds/gmxapi/build:${PYTHONPATH}"
export PATH PYTHONPATH
%labels
AUTHOR jmh5sf@virginia.edu
%post
apt-get update && apt-get -y install libopenmpi-dev libfftw3-dev cmake make git python3-dev python3-pip locales
# Install python dependencies
pip3 install setuptools networkx cmake mpi4py numpy scipy
mkdir /builds
cd /builds
# gromacs-gmxapi
git clone https://github.com/kassonlab/gromacs-gmxapi.git
cd gromacs-gmxapi
git checkout tags/v0.0.6 -b v0.0.6
mkdir build
cd build
cmake ../ -DGMX_MPI=OFF -DGMX_GPU=ON -DGMX_OPENMP=ON -DGMX_USE_NVML=OFF
make -j8; make install
cd /builds
# gmxapi
git clone https://github.com/kassonlab/gmxapi.git
cd gmxapi
git checkout tags/v0.0.6 -b v0.0.6
mkdir build; cd build
cmake ../ -Dgmxapi_DIR=/usr/local/gromacs/share/cmake/gmxapi
make -j8; make install
cd /builds
# Get BRER plugin
git clone https://github.com/jmhays/sample_restraint.git
cd sample_restraint
git checkout deer
mkdir build; cd build
cmake ../ -Dgmxapi_DIR=/usr/local/gromacs/share/cmake/gmxapi -DGROMACS_DIR=/usr/local/gromacs/share/cmake/gromacs
make -j8; make install
cd /builds
# BRER run scripts
git clone https://github.com/jmhays/run_brer.git
cd run_brer/
git checkout devel
python3 setup.py install
Collection
- Name: jmhays/singularity-brer
- License: GNU Lesser General Public License v2.1
View on Datalad
Metrics
key | value |
---|---|
id | /containers/jmhays-singularity-brer-latest |
collection name | jmhays/singularity-brer |
branch | devel |
tag | latest |
commit | 87b01a51be400ca6fdee85dfb48821e4ed07129c |
version (container hash) | 0797ea6555bc976a64127029dd9176ca |
build date | 2018-10-25T20:56:45.017Z |
size (MB) | 2722 |
size (bytes) | 1449627679 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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