nbcrrolls/electrostatics-singularity:latest
$ singularity pull shub://nbcrrolls/electrostatics-singularity:latest
Singularity Recipe
#################################################################################
# Singularity Definition File
#
# Version: 2.1
# Software: Molecular electrostatics singularity image
# Software Version: 2019.4.23
# Description: Docker image for BrownDye, APBS and PDB2PQR
# Website: https://browndye.ucsd.edu
# Github: https://github.com/nbcrrolls/electrostatics-singularity
# Tags: Electrostatics|Brownian Dynamics|Solvation
# Build command: singularity build electrostatics.simg Singularity
# Pull command: singularity pull shub://nbcrrolls/electrostatics-singularity
# Run command: singularity shell nbcrrolls-electrostatics-singularity-master-latest.simg
# Run command: singularity exec [image name] apbs input.in
# Run command: singularity run --app apbs [image name] arguments
# Run command: singularity run --app pdb2pqr [image name] arguments
#
#################################################################################
Bootstrap: debootstrap
MirrorURL: http://us.archive.ubuntu.com/ubuntu
OSVersion: xenial # 16.04
#Bootstrap: docker
#From: ubuntu:16.04
%labels
APPLICATION_NAME apbs-pdb2pqr-browndye
APPLICATION_VERSION 1.5 + 2.1.0 + 2.0
APPLICATION_URL http://www.poissonboltzmann.org + https://browndye.ucsd.edu
SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 1024
ORIGINAL_AUTHOR_NAME Robert Konecny
ORIGINAL_AUTHOR_EMAIL rok@ucsd.edu
ORIGINAL_DEFINITION_FILE https://github.com/nbcrrolls/electrostatics-singularity/blob/master/Singularity
MODIFYING_AUTHOR_NAME Marty Kandes
MODIFYING_AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20190423
%help
This is a singularity image with molecular electrostatics tools:
apbs, pdb2pqr and BrownDye. All applications are intalled in /opt
sub-directories and are in your $PATH.
%runscript
# this will get copied to /.singularity.d/runscript indide the container
# which will run whenever the container is called as an executable
#if [ $# -eq 0 ]
#then
echo
echo "========================================================================="
echo " This container includes the following apps:"
echo
echo " APBS v1.5 https://www.poissonboltzmann.org"
echo " PDB2PQR v2.1.0 https://www.poissonboltzmann.org"
echo " BrownDye v2.0 https://browndye.ucsd.edu"
echo
echo " Please register your use of APBS and PDB2PQR at http://eepurl.com/by4eQr"
echo
echo " To list all available applications do 'singularity apps [image name]'"
echo "========================================================================="
echo
#else
echo "Executing arguments: $*"
exec "$@"
#fi
%post -c /bin/bash
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
set -o errexit
#
APBS_VERSION=1.5
PDB2PQR_VERSION=2.1.0
BD1_VERSION="1.0-13_Feb_2019"
BD2_VERSION="2.0-11_Mar_2019"
#
#APBS_URL=https://versaweb.dl.sourceforge.net/project/apbs/apbs/apbs-${APBS_VERSION}
APBS_URL=https://downloads.sourceforge.net/apbs
APBS_PKG=APBS-${APBS_VERSION}-linux64
#PDB2PQR_URL=https://versaweb.dl.sourceforge.net/project/pdb2pqr/pdb2pqr/pdb2pqr-${PDB2PQR_VERSION}
PDB2PQR_URL=https://downloads.sourceforge.net/pdb2pqr
PDB2PQR_PKG=pdb2pqr-linux-bin64-${PDB2PQR_VERSION}
BD_URL=https://browndye.ucsd.edu
BD1_PKG=browndye.tar.gz
BD2_PKG=browndye2.tar.gz
OCAML_VERSION=4.06
OCAML_VERSION_MINOR=0
OCAML_PKG=ocaml-${OCAML_VERSION}.${OCAML_VERSION_MINOR}
OCAML_URL=http://caml.inria.fr/pub/distrib/ocaml-${OCAML_VERSION}
# needed for Ubuntu 18.04 (Bionic)
#RL_URL=https://mirrors.edge.kernel.org/ubuntu/pool/main/r/readline6
#RL_PKG=libreadline6_6.3-8ubuntu8_amd64.deb
DEBIAN_FRONTEND=noninteractive
apt-get -y install ubuntu-standard
apt-get -y install software-properties-common
add-apt-repository universe
# Upgrade all packages to their latest versions
apt-get -y update && apt-get -y upgrade
apt-get -y install build-essential
apt-get -y install curl
#apt-get -y install ocaml
apt-get -y install libexpat-dev
apt-get -y install libgfortran3
apt-get -y install libboost-dev
apt-get -y install liblapack-dev
# works with Ubuntu 16.04 (Xenial)
apt-get -y install libreadline6
# needs 'universe' repo for modules
apt-get -y install environment-modules
cd /tmp
wget -qO - ${OCAML_URL}/${OCAML_PKG}.tar.gz | tar xzf -
cd ${OCAML_PKG}
./configure
make world.opt
umask 022
make install
rm -rf /tmp/${OCAML_PKG}
#curl -k ${BD_URL}/${BD1_PKG} | tar xzf - -C /opt
wget -qO - ${BD_URL}/${BD1_PKG} | tar xzf - -C /opt
cd /opt/browndye
#curl -k -sO ${BD_URL}/browndye/doc/fixes.html
wget -q ${BD_URL}/browndye/doc/fixes.html
make all
wget -qO - ${BD_URL}/${BD2_PKG} | tar xzf - -C /opt
cd /opt/browndye2
wget -q ${BD_URL}/browndye2/doc/fixes.html
make all
mkdir lib && cd lib
wget -q ${BD_URL}/coffdrop.xml.gz
wget -q ${BD_URL}/connectivity.xml
wget -q ${BD_URL}/map.xml
wget -q ${BD_URL}/charges.xml
# needed for Ubuntu 18.04 (Bionic)
#curl -k ${RL_URL}/${RL_PKG} -o /tmp/${RL_PKG}
#dpkg -i /tmp/${RL_PKG}
apt-get -y purge gcc
apt-get -y purge g++
#apt-get -y purge ocaml
apt-get -y purge libexpat-dev
apt-get -y purge libboost-dev
apt-get -y purge liblapack-dev
apt-get -y clean && apt-get -y autoremove
rm -rf /var/lib/apt/lists/*
# add apbs
wget -qO- --no-check-certificate ${APBS_URL}/${APBS_PKG}.tar.gz | tar xzf - -C /opt
ln -s /opt/${APBS_PKG} /opt/apbs
# add pdb2pqr
wget -qO- --no-check-certificate ${PDB2PQR_URL}/${PDB2PQR_PKG}.tar.gz | tar xzf - -C /opt
ln -s /opt/${PDB2PQR_PKG} /opt/pdb2pqr
# add modules to /usr/share/modules/modulefiles
ln -s /usr/share/modules /usr/share/Modules
MODULE_PATH=/usr/share/modules/modulefiles
echo "#%Module1.0" > ${MODULE_PATH}/browndye1
echo "conflict browndye2" >> ${MODULE_PATH}/browndye1
echo "prepend-path PATH /opt/browndye/bin" >> ${MODULE_PATH}/browndye1
echo "#%Module1.0" > ${MODULE_PATH}/browndye2
echo "conflict browndye1" >> ${MODULE_PATH}/browndye2
echo "prepend-path PATH /opt/browndye2/bin" >> ${MODULE_PATH}/browndye2
# stupid ubuntu/dash
rm /bin/sh
ln -s /bin/bash /bin/sh
# Make filesystem mount points
mkdir /cvmfs /oasis /projects /scratch
%environment
# Set system locale
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
. /etc/profile.d/modules.sh
export -f module
# Set APBS, PDB2PQR, and BrownDye environment variables
export APBS_VERSION=1.5
export APBS_PATH=/opt/apbs
export PDB2PQR_VERSION=2.1.0
export PDB2PQR_PATH=/opt/pdb2pqr
export BD1_VERSION="1.0-13_Feb_2019"
export BD1_PATH=/opt/browndye
export BD2_VERSION="2.0-11_Mar_2019"
export BD2_PATH=/opt/browndye2
export PATH=${APBS_PATH}/bin:${PDB2PQR_PATH}:${PATH}
export LD_LIBRARY_PATH=${APBS_PATH}/lib
%apphelp apbs
apbs version 1.5
For instructions on use see http://www.poissonboltzmann.org/
Please register your use of APBS and PDB2PQR at http://eepurl.com/by4eQr
apbs is installed in /opt/apbs
%apprun apbs
/opt/apbs/bin/apbs "$@"
%apphelp pdb2pqr
pdb2pqr version 2.1.0
For instructions on use see http://www.poissonboltzmann.org/
pdb2pqr is installed in /opt/pdb2pqr
%apprun pdb2pqr
/opt/pdb2pqr/pdb2pqr "$@"
%apphelp nam_simulation
BrownDye version 1 and 2
For instructions on use see https://browndye.ucsd.edu
All BrowDye programs are installed in /opt/browndye{1:2}/bin
%apprun nam_simulation
/opt/browndye2/bin/nam_simulation "$@"
%apphelp we_simulation
BrownDye version 1 and 2
For instructions on use see https://browndye.ucsd.edu
All BrowDye programs are installed in /opt/browndye{1:2}/bin
%apprun we_simulation
/opt/browndye2/bin/we_simulation "$@"
#%apphelp pqr2xml
#
# BrownDye version 2.0
# For instructions on use see https://browndye.ucsd.edu
#
#%apprun pqr2xml
#
# /opt/browndye2/bin/pqr2xml "$@"
#%apphelp make_rxn_pairs
#
# BrownDye version 2.0
# For instructions on use see https://browndye.ucsd.edu
#
#%apprun make_rxn_pairs
#
# /opt/browndye2/bin/make_rxn_pairs "$@"
#%apphelp xyz_trajectory
#
# BrownDye version 2.0
# For instructions on use see https://browndye.ucsd.edu
#
#%apprun xyz_trajectory
#
# /opt/browndye2/bin/xyz_trajectory "$@"
Collection
View on Datalad
Metrics
key | value |
---|---|
id | /containers/nbcrrolls-electrostatics-singularity-latest |
collection name | nbcrrolls/electrostatics-singularity |
branch | master |
tag | latest |
commit | 3f5a54813e2b9149bb4d3f7539fe74d160c980b5 |
version (container hash) | 8adb503feec490761a06bd9291463da2 |
build date | 2019-04-23T20:55:37.981Z |
size (MB) | 1183 |
size (bytes) | 427544607 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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