Updated sourceforge links.

Cleanup.
nbcrrolls · Apr 22, 2019 · 23b161a · 23b161a
1 parent 0996e4e
commit 23b161a
Showing 1 changed file with 34 additions and 32 deletions.
diff --git a/Singularity b/Singularity
@@ -3,9 +3,10 @@
 # 
 # Version:          2.0
 # Software:         Molecular electrostatics singularity image
-# Software Version: 2019.4.16
+# Software Version: 2019.4.22
 # Description:      Docker image for BrownDye, APBS and PDB2PQR
-# Website:          http://browndye.ucsd.edu
+# 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
@@ -42,7 +43,7 @@ OSVersion: xenial # 16.04
     MODIFYING_AUTHOR_NAME Marty Kandes
     MODIFYING_AUTHOR_EMAIL mkandes@sdsc.edu
 
-    LAST_UPDATED 20190417
+    LAST_UPDATED 20190422
 
 %help
 
@@ -75,21 +76,27 @@ OSVersion: xenial # 16.04
 #fi
 
 %post -c /bin/bash
-    # Set system locale
     export LC_ALL=C
     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="2.0-11_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
@@ -100,43 +107,39 @@ OSVersion: xenial # 16.04
     apt-get -y update && apt-get -y upgrade
     apt-get -y install build-essential
     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
     # works with Ubuntu 16.04 (Xenial)
     apt-get -y install libreadline6
-    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
+    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
+    #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
+    #curl -k -sO ${BD_URL}/browndye/doc/fixes.html
+    wget -q ${BD_URL}/browndye/doc/fixes.html
     make all
 
-    curl -k ${BD_URL}/${BD2_PKG} | tar xzf - -C /opt
+    wget -qO - ${BD_URL}/${BD2_PKG} | tar xzf - -C /opt
     cd /opt/browndye2
-    curl -k -sO ${BD_URL}/browndye2/doc/fixes.html
+    wget -q ${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
+    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}
@@ -149,16 +152,15 @@ OSVersion: xenial # 16.04
     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
+    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 -q --no-check-certificate ${PDB2PQR_URL}/${PDB2PQR_PKG} -O - | tar xzf - -C /opt
-    ln -s /opt/pdb2pqr-linux-bin64-${PDB2PQR_VERSION} /opt/pdb2pqr
+    wget -qO- --no-check-certificate ${PDB2PQR_URL}/${PDB2PQR_PKG}.tar.gz | tar xzf - -C /opt
+    ln -s /opt/${PDB2PQR_PKG} /opt/pdb2pqr
 
     # Make filesystem mount points
     mkdir /cvmfs /oasis /projects /scratch