naked-singularity-v0.6.5 :: added new apbs-pdb2pqr-browndye.def for

comet in order to support browndye2-based calculations

README

@@ -46,8 +46,8 @@ AUTHOR
 
 VERSION
 
-    0.6.4
+    0.6.5
 
 LAST UPDATED
 
-    Wednesday, March 27th, 2019
+    Tuesday, April 2nd, 2019

definition-files/comet/apbs-pdb2pqr-browndye/README.md

+# Singularity container for molecular electrostatic calculations using PDB2PQR/APBS and Brownian dynamics with BrownDye.
+
+This singularity image contains a complete software environment for running [BrownDye (version 1 and 2)](http://browndye.ucsd.edu/) simulations. It also includes [PDB2PQR](http://www.poissonboltzmann.org/) and [APBS](http://www.poissonboltzmann.org/).
+
+Please [register](http://eepurl.com/by4eQr) your use of APBS and PDB2PQR.
+
+## Using the container
+
+Pull the singularity image:
+```
+singularity pull shub://nbcrrolls/electrostatics-singularity
+```
+
+Start bash shell in the container:
+```
+singularity shell nbcrrolls-electrostatics-singularity-master-latest.simg
+```
+
+Now the container is running and we can start a BrownDye2 job (using the Thrombin example):
+
+```
+cp -ai $BD2_PATH/examples/thrombin .
+cd thrombin
+sed -i 's/-PE0//g' *
+make all
+```
+
+And if you want to use BrownDye version 1:
+
+```
+export PATH=$BD1_PATH/bin:$PATH
+cp -ai $BD1_PATH/thrombin-example .
+cd thrombin-example
+sed -i 's/-PE0//g' *
+make all
+bd_top input.xml
+nam_simulation t-m-simulation.xml # this takes about 20min to run
+cat results.xml
+```
+After we are finished we can quit the container:
+
+    exit
+
+You can also access individual applications from the electrostatics container.
+
+To list available applications:
+
+```
+$ singularity apps nbcrrolls-electrostatics-singularity-master-latest.simg 
+apbs
+make_rxn_pairs
+nam_simulation
+pdb2pqr
+pqr2xml
+we_simulation
+xyz_trajectory
+```
+
+To run, for example, apbs calculation:
+```
+singularity exec nbcrrolls-electrostatics-singularity-master-latest.simg apbs input.in
+```
+
+or
+
+```
+singularity run --app apbs nbcrrolls-electrostatics-singularity-master-latest.simg input.in
+```
+
+
+This Singularity image is hosted on Singularity Hub: [![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/2497)
+
+
+
+###### This project is supported by [NBCR](http://nbcr.ucsd.edu).

definition-files/comet/apbs-pdb2pqr-browndye/apbs-pdb2pqr-browndye.def

+################################################################################# 
+# Singularity Definition File
+# 
+# Version:          2.0
+# Software:         Molecular electrostatics singularity image
+# Software Version: 2019.3.7
+# Description:      Docker image for BrownDye, APBS and PDB2PQR
+# Website:          http://browndye.ucsd.edu
+# 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: 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_SINGULAIRTY_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 20190402
+
+%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 $PATH.
+
+%runscript
+
+    cat << EOF
+
+    This container includes the following apps:
+
+        APBS v1.5 - http://www.poissonboltzmann.org/
+        PDB2PQR v2.1.0 - http://www.poissonboltzmann.org/
+        BrownDye v2.0 (26 Feb 2019) - https://browndye.ucsd.edu/
+
+    Please register your use of APBS and PDB2PQR at http://eepurl.com/by4eQr
+
+    To list all available applications do "singularity apps [image name]"
+
+    EOF
+
+%post -c /bin/bash
+
+    set -o errexit
+    APBS_VERSION=1.5
+    PDB2PQR_VERSION=2.1.0
+    APBS_URL=https://versaweb.dl.sourceforge.net/project/apbs/apbs/apbs-${APBS_VERSION}
+    APBS_PKG=APBS-${APBS_VERSION}-linux64.tar.gz
+    PDB2PQR_URL=https://versaweb.dl.sourceforge.net/project/pdb2pqr/pdb2pqr/pdb2pqr-${PDB2PQR_VERSION}
+    PDB2PQR_PKG=pdb2pqr-linux-bin64-${PDB2PQR_VERSION}.tar.gz
+    BD1_VERSION="1.0-13-Feb_2019"
+    BD2_VERSION="2.0-26_Feb_ 2019"                                                                                                    
+    BD_URL=https://browndye.ucsd.edu
+    BD1_PKG=browndye.tar.gz
+    BD2_PKG=browndye2.tar.gz
+    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 update
+    apt-get -y install curl 
+    apt-get -y install make 
+    apt-get -y install gcc 
+    apt-get -y install g++ 
+    #apt-get -y install ocaml
+    apt-get -y install libexpat-dev 
+    apt-get -y install nano 
+    apt-get -y install readline-common
+    apt-get -y install libgfortran3 
+    apt-get -y install wget 
+    apt-get -y install libboost-dev 
+    apt-get -y install liblapack-dev
+
+    cd /tmp
+
+    wget http://caml.inria.fr/pub/distrib/ocaml-4.06/ocaml-4.06.0.tar.gz
+    tar -xzvf ocaml-4.06.0.tar.gz
+    cd ocaml-4.06.0
+    ./configure
+    make world.opt
+    umask 022
+    make install
+
+    curl -k ${BD_URL}/${BD1_PKG} | tar xzf - -C /opt
+    cd /opt/browndye
+    curl -k -sO ${BD_URL}/browndye/doc/fixes.html
+    make all
+
+    curl -k ${BD_URL}/${BD2_PKG} | tar xzf - -C /opt
+    cd /opt/browndye2
+    curl -k -sO ${BD_URL}/browndye2/doc/fixes.html
+    make all
+    mkdir lib && cd lib
+    curl -k -sO ${BD_URL}/coffdrop.xml.gz
+    curl -k -sO ${BD_URL}/connectivity.xml
+    curl -k -sO ${BD_URL}/map.xml
+    curl -k -sO ${BD_URL}/charges.xml
+
+    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 clean
+    apt-get -y autoremove
+    apt-get -y install ca-certificates
+    rm -rf /var/lib/apt/lists/*
+
+    # add apbs
+    wget -q --no-check-certificate ${APBS_URL}/${APBS_PKG} -O - | tar xzf - -C /opt
+    ln -s /opt/APBS-${APBS_VERSION}-linux64 /opt/apbs
+
+    # add pdb2pqr
+    wget -q --no-check-certificate ${PDB2PQR_URL}/${PDB2PQR_PKG} -O - | tar xzf - -C /opt
+    ln -s /opt/pdb2pqr-linux-bin64-${PDB2PQR_VERSION} /opt/pdb2pqr
+
+%environment
+
+    # Set system locale
+    export LC_ALL=C
+
+    # Set APBS, PDB2PQR, and BrownDye environment variables
+    export APBS_VERSION=1.5
+    export APBS_PATH=/opt/apbs
+
+    export PDB2PQR_VERSION=2.1.0
+    export PDB2PQR_PATH=/opt/pdb2pqr
+
+    export BD1_VERSION="1.0-13-Feb_2019"
+    export BD1_PATH=/opt/browndye
+
+    export BD2_VERSION="2.0-26_Feb_ 2019"
+    export BD2_PATH=/opt/browndye2
+
+    export PATH=${APBS_PATH}/bin:${PDB2PQR_PATH}:${BD2_PATH}/bin:$PATH
+    export LD_LIBRARY_PATH=${APBS_PATH}/lib
+
+%apphelp apbs
+
+    apbs version 1.5
+    For instructions on use see http://www.poissonboltzmann.org/
+    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 2.0 (26 Feb 2019)
+    For instructions on use see https://browndye.ucsd.edu
+    All BrowDye programs are installed in /opt/browndye/bin
+
+%apprun nam_simulation
+
+    /opt/browndye2/bin/nam_simulation "$@"
+
+%apphelp pqr2xml
+
+    BrownDye version 2.0 (26 Feb 2019)
+    For instructions on use see https://browndye.ucsd.edu
+
+%apprun pqr2xml
+
+    /opt/browndye2/bin/pqr2xml "$@"
+
+%apphelp make_rxn_pairs
+
+   BrownDye version 2.0 (26 Feb 2019)
+   For instructions on use see https://browndye.ucsd.edu
+
+%apprun make_rxn_pairs
+
+   /opt/browndye2/bin/make_rxn_pairs "$@"
+
+%apphelp we_simulation
+
+   BrownDye version 2.0 (26 Feb 2019)
+   For instructions on use see https://browndye.ucsd.edu
+
+%apprun we_simulation
+
+   /opt/browndye2/bin/we_simulation "$@"
+
+%apphelp xyz_trajectory
+
+   BrownDye version 2.0 (26 Feb 2019)
+   For instructions on use see https://browndye.ucsd.edu
+
+%apprun xyz_trajectory
+
+   /opt/browndye2/bin/xyz_trajectory "$@"

naked-singularity.sh

@@ -248,7 +248,7 @@ naked_install() {
 
   local operating_system='ubuntu'
   local prefix='/usr/local'
-  local version='2.5.2'
+  local version='2.6.1'
 
   naked_out "Read in all command-line options of the 'install' command ..."