Update adt

astrocyte-adt/Dockerfile

 FROM git.biohpc.swmed.edu:5050/astrocyte/container/astrocyte-viz-base:ubuntu-18
 
-ARG ARG_HOME="/home/headless"
-ARG STARTUPDIR="/dockerstartup"
-ARG LOG_FOLDER="/tmp/astrocyte-adt"
 ARG ADT_VERSION="1.5.7p1"
 ARG AUTODOCK_VERSION="4.2.6"
 ARG VINA_VERSION="1.2.3"
 
-ENV LANG en_US.UTF-8
-ENV HOME=${ARG_HOME:-/home/headless}
-ENV PW=${ARG_PW:-headless}
-ENV STARTUPDIR="/dockerstartup"
-ENV DISPLAY=":6"
-ENV VNC_PORT="5906"
-ENV VNC_RESOLUTION="1280x1024"
-ENV VNC_BLACKLIST_THRESHOLD=-20
-ENV VNC_BLACKLIST_TIMEOUT=-0
-ENV VNC_COL_DEPTH=24
-ENV LOG_FOLDER=${LOG_FOLDER:-"/tmp/astrocyte-adt"}
-ENV NO_VNC_HOME="/usr/share/usr/local/share/noVNCdim"
-ENV NO_VNC_PORT="6900"
 ENV ADT_VERSION="${ADT_VERSION:-1.5.7p1}"
 ENV AUTODOCK_VERSION="${AUTODOCK_VERSION:-4.2.6}"
 ENV VINA_VERSION="${VINA_VERSION:-1.2.3}"
@@ -30,11 +14,15 @@ COPY ["./src/run_docking", "/usr/local/bin/"]
 RUN apt-get update && \
     DEBIAN_FRONTEND="noninteractive" apt-get install -y --no-install-recommends \
     build-essential \
+    csh \
     apt-utils \
     curl \
     openbabel \
     && \
     \
+    # set default python to python3
+    update-alternatives --install /usr/bin/python python /usr/bin/python3 1 && \
+    \
     # MGLtoos
     curl https://ccsb.scripps.edu/mgltools/download/491/ --output mgltools-${ADT_VERSION}.tar.gz && \
     tar zxf mgltools-${ADT_VERSION}.tar.gz && \
@@ -44,7 +32,7 @@ RUN apt-get update && \
     cat initMGLtools.sh >> /etc/profile && \
     cd && \
     \
-    # Autodock
+    # Autodock & Autogrid
     curl https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/autodocksuite-${AUTODOCK_VERSION}-x86_64Linux2.tar --output autodock-${AUTODOCK_VERSION}.tar && \
     tar xf autodock-${AUTODOCK_VERSION}.tar && \
     mv x86_64Linux2/auto* /usr/local/bin && \

astrocyte-adt/build_singularity.sh

@@ -11,10 +11,6 @@ BIOHPC_REGISTRY="git.biohpc.swmed.edu:5050/astrocyte/container"
 # build docker
 sudo docker build -t ${REGISTRY}/${REPO}:${TAG} .
 
-# # push to registry
-# sudo docker login
-# sudo docker push ${REGISTRY}/${REPO}:${TAG}
-
 # push to BioHPC
 export DOCKER_BUILDKIT=0
 export COMPOSE_DOCKER_CLI_BUILD=0
@@ -30,7 +26,6 @@ else
     TAGL=$TAG
 fi
 
-
 # build singularity
 sudo docker save ${REGISTRY}/${REPO}:${TAG} > ${REPO}_${TAG}.tar
 rm -fr ${REPO}_${TAGL}.sif

astrocyte-adt/run_singularity.sh

@@ -2,32 +2,10 @@
 REPO="astrocyte-adt"
 TAG="latest"
 
-# Set the DISPLAY
-DISPLAY=":6"
-used_ports=$(lsof -i -P -n | grep TCP | awk -F: '{print $NF}' | awk '{print $1}' | sort -un)
-for i in $(seq 6 99); do
-    if echo $used_ports | grep -w $(expr 5900 + $i) > /dev/null; then
-        continue
-    else
-        DISPLAY=":$i";
-        break
-    fi
-done
-
-# Set novnc http port
-for i in $(seq 0 99); do
-    NO_VNC_PORT=$(expr 6900 + $i)
-    if echo $used_ports | grep -w $NO_VNC_PORT > /dev/null; then
-        continue
-    else
-        break
-    fi
-done
-
 # Prepare log file locations
 calling_username=$(id -un)
 host_name=$(hostname -s)
-logfolder=/tmp/astrocyte-adt-${host_name}-${calling_username}-$(echo $DISPLAY | tr -d ":")
+logfolder=/tmp/astrocyte-adt-${host_name}-${calling_username}-$(date +%s)
 rm -fr $logfolder
 mkdir -p $logfolder/$calling_username
 mkdir -p $logfolder/run
@@ -35,7 +13,7 @@ mkdir -p $logfolder/var/log
 chmod -R 777 $logfolder
 chmod 700 $logfolder
 
-AUTOSTART_COMMAND="xfce4-terminal -e /usr/local/adt/mgltools-1.5.7p1/bin/adt"
+AUTOSTART_COMMAND="cd $outputDir; xfce4-terminal -e /usr/local/adt/mgltools-1.5.7p1/bin/adt"
 
 # Prepare the bind string 
 bind_strings="$logfolder/run:/run,$logfolder/var/log:/var/log"
@@ -51,8 +29,7 @@ fi
 echo "source /etc/profile" > $logfolder/$calling_username/.bashrc
 
 # mount and run
-SINGULARITYENV_DISPLAY="$DISPLAY" \
-SINGULARITYENV_NO_VNC_PORT="$NO_VNC_PORT" \
+SINGULARITYENV_NO_VNC_PORT="${VIZAPP_PORT:-$NO_VNC_PORT}" \
 SINGULARITYENV_AUTOSTART_COMMAND="$AUTOSTART_COMMAND" \
 SINGULARITYENV_LOG_FOLDER="$logfolder" \
 singularity run --nv -e \