From ec83bac7040f1278f723e1d8a84b98bba6f74b33 Mon Sep 17 00:00:00 2001 From: Marty Kandes <mkandes@sdsc.edu> Date: Tue, 2 Apr 2019 16:27:31 -0700 Subject: [PATCH] naked-singularity-v0.6.5 :: added new apbs-pdb2pqr-browndye.def for comet in order to support browndye2-based calculations --- README | 4 +- .../comet/apbs-pdb2pqr-browndye/README.md | 75 ++++++ .../apbs-pdb2pqr-browndye.def | 228 ++++++++++++++++++ naked-singularity.sh | 2 +- 4 files changed, 306 insertions(+), 3 deletions(-) create mode 100644 definition-files/comet/apbs-pdb2pqr-browndye/README.md create mode 100644 definition-files/comet/apbs-pdb2pqr-browndye/apbs-pdb2pqr-browndye.def diff --git a/README b/README index 2f308c3..81a4b44 100644 --- a/README +++ b/README @@ -46,8 +46,8 @@ AUTHOR VERSION - 0.6.4 + 0.6.5 LAST UPDATED - Wednesday, March 27th, 2019 + Tuesday, April 2nd, 2019 diff --git a/definition-files/comet/apbs-pdb2pqr-browndye/README.md b/definition-files/comet/apbs-pdb2pqr-browndye/README.md new file mode 100644 index 0000000..c8fbaea --- /dev/null +++ b/definition-files/comet/apbs-pdb2pqr-browndye/README.md @@ -0,0 +1,75 @@ +# 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://singularity-hub.org/collections/2497) + + + +###### This project is supported by [NBCR](http://nbcr.ucsd.edu). diff --git a/definition-files/comet/apbs-pdb2pqr-browndye/apbs-pdb2pqr-browndye.def b/definition-files/comet/apbs-pdb2pqr-browndye/apbs-pdb2pqr-browndye.def new file mode 100644 index 0000000..7e4da27 --- /dev/null +++ b/definition-files/comet/apbs-pdb2pqr-browndye/apbs-pdb2pqr-browndye.def @@ -0,0 +1,228 @@ +################################################################################# +# 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 "$@" diff --git a/naked-singularity.sh b/naked-singularity.sh index 1b0923b..e7d1fb3 100755 --- a/naked-singularity.sh +++ b/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 ..." -- GitLab