Fix FTP docker and timezone in docker images/containers

src/Docker/alaska/Dockerfile

@@ -2,6 +2,11 @@
 # UBUNTU VERSION: 16.04 (xenial)
 FROM ubuntu:xenial
 
+# Timezone
+ARG TIMEZONE=America/Los_Angeles
+RUN ln -snf /usr/share/zoneinfo/$TIMEZONE /etc/localtime && \
+    echo $TIMEZONE > /etc/timezone
+
 # default to 4.5.1
 ARG MINICONDA_VER=4.5.1
 ARG MINICONDA3_URL=https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-Linux-x86_64.sh

src/Docker/alaska/build_image.sh

@@ -5,8 +5,10 @@ source scripts/set_env_variables.sh
 
 # build alaska image
 docker build -t $DOCKER_ALASKA_TAG \
+             --build-arg TIMEZONE=$TIMEZONE \
              --build-arg MINICONDA_VER="$MINICONDA_VER" \
              --build-arg MINICONDA3_URL="$MINICONDA3_URL" \
+             --force-rm \
              --no-cache \
              Docker/alaska/
 

src/Docker/cgi/Dockerfile

@@ -2,6 +2,11 @@
 # UBUNTU VERSION: 16.04 (xenial)
 FROM ubuntu:xenial
 
+# Timezone
+ARG TIMEZONE=America/Los_Angeles
+RUN ln -snf /usr/share/zoneinfo/$TIMEZONE /etc/localtime && \
+    echo $TIMEZONE > /etc/timezone
+
 ##### DEPENDECIES #####
 RUN apt-get update && apt-get install -y \
     lsb-release \

src/Docker/cgi/build_image.sh

@@ -5,6 +5,8 @@ source scripts/set_env_variables.sh
 
 # build cgi image
 docker build -t $DOCKER_CGI_TAG \
+             --build-arg TIMEZONE=$TIMEZONE \
+             --force-rm \
              --no-cache \
              Docker/cgi/
 

src/Docker/ftp/build_container.sh

@@ -4,14 +4,13 @@ source scripts/set_env_variables.sh
 
 # create ftp container
 docker create -it --name="$DOCKER_FTP_TAG" \
-              -v $DOCKER_TIME_MOUNT \
               -v $DOCKER_DATA_MOUNT \
               -v $DOCKER_FTP_MOUNT \
               -p $DOCKER_FTP_PORT \
               -p $DOCKER_FTP_PORTS \
-              -e "$DOCKER_FTP_ENV1" \
-              -e "$DOCKER_FTP_ENV2" \
-              -e "$DOCKER_FTP_ENV3" \
+              -e "$DOCKER_FTP_HOST" \
+              -e "$DOCKER_FTP_FLAGS" \
+              -e "TZ=$TIMEZONE" \
               --restart unless-stopped \
               $DOCKER_FTP_BASE
 

src/Docker/kallisto/Dockerfile

@@ -2,6 +2,11 @@
 # UBUNTU VERSION: 16.04 (xenial)
 FROM ubuntu:xenial
 
+# Timezone
+ARG TIMEZONE=America/Los_Angeles
+RUN ln -snf /usr/share/zoneinfo/$TIMEZONE /etc/localtime && \
+    echo $TIMEZONE > /etc/timezone
+
 # versions
 ARG MINICONDA_VER=4.5.1
 ARG MINICONDA3_URL=https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-Linux-x86_64.sh

src/Docker/kallisto/build_image.sh

@@ -4,10 +4,12 @@ source scripts/set_env_variables.sh
 
 # build kallisto image
 docker build -t $DOCKER_KALLISTO_TAG \
+             --build-arg TIMEZONE="$TIMEZONE" \
              --build-arg MINICONDA_VER="$MINICONDA_VER" \
              --build-arg MINICONDA3_URL="$MINICONDA3_URL" \
              --build-arg KALLISTO_VER="$KALLISTO_VER" \
              --build-arg KALLISTO_URL="$KALLISTO_URL" \
+             --force-rm \
              --no-cache \
              Docker/kallisto/
 

src/Docker/qc/Dockerfile

@@ -2,6 +2,11 @@
 # UBUNTU VERSION: 16.04 (xenial)
 FROM ubuntu:xenial
 
+# Timezone
+ARG TIMEZONE=America/Los_Angeles
+RUN ln -snf /usr/share/zoneinfo/$TIMEZONE /etc/localtime && \
+    echo $TIMEZONE > /etc/timezone
+
 # versions
 # Note: rseqc requires python2
 ARG MINICONDA_VER=4.5.1

src/Docker/qc/build_image.sh

@@ -4,6 +4,7 @@ source scripts/set_env_variables.sh
 
 # build qc image
 docker build -t $DOCKER_QC_TAG \
+             --build-arg TIMEZONE="$TIMEZONE" \
              --build-arg MINICONDA_VER="$MINICONDA_VER" \
              --build-arg MINICONDA2_URL="$MINICONDA2_URL" \
              --build-arg BOWTIE2_VER="$BOWTIE2_VER" \
@@ -14,6 +15,7 @@ docker build -t $DOCKER_QC_TAG \
              --build-arg SAMBAMBA_VER="$SAMBAMBA_VER" \
              --build-arg KALLISTO_VER="$KALLISTO_VER" \
              --build-arg KALLISTO_URL="$KALLISTO_URL" \
+             --force-rm \
              --no-cache \
              Docker/qc/
 

src/Docker/request/Dockerfile

@@ -2,6 +2,11 @@
 # UBUNTU VERSION: 16.04 (xenial)
 FROM ubuntu:xenial
 
+# Timezone
+ARG TIMEZONE=America/Los_Angeles
+RUN ln -snf /usr/share/zoneinfo/$TIMEZONE /etc/localtime && \
+    echo $TIMEZONE > /etc/timezone
+
 # default to 4.5.1
 ARG MINICONDA_VER=4.5.1
 ARG MINICONDA3_URL=https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-Linux-x86_64.sh

src/Docker/request/build_image.sh

@@ -4,9 +4,11 @@ source scripts/set_env_variables.sh
 
 # build request image
 docker build -t $DOCKER_REQUEST_TAG \
+             --build-arg TIMEZONE="$TIMEZONE" \
              --build-arg MINICONDA_VER="$MINICONDA_VER" \
              --build-arg MINICONDA3_URL="$MINICONDA3_URL" \
              --no-cache \
+             --force-rm \
              Docker/request/
 
 # exit with return value of the above command

src/Docker/sleuth/Dockerfile

@@ -2,6 +2,11 @@
 # UBUNTU VERSION: 16.04 (xenial)
 FROM ubuntu:xenial
 
+# Timezone
+ARG TIMEZONE=America/Los_Angeles
+RUN ln -snf /usr/share/zoneinfo/$TIMEZONE /etc/localtime && \
+    echo $TIMEZONE > /etc/timezone
+
 # default to 4.5.1
 ARG MINICONDA_VER=4.5.1
 ARG MINICONDA3_URL=https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-Linux-x86_64.sh

src/Docker/sleuth/build_image.sh

@@ -4,10 +4,12 @@ source scripts/set_env_variables.sh
 
 # build request image
 docker build -t $DOCKER_SLEUTH_TAG \
+             --build-arg TIMEZONE="$TIMEZONE" \
              --build-arg MINICONDA_VER="$MINICONDA_VER" \
              --build-arg MINICONDA3_URL="$MINICONDA3_URL" \
              --build-arg SLEUTH_VER="$SLEUTH_VER" \
              --no-cache \
+             --force-rm \
              Docker/sleuth/
 
 # exit with return value of the above command

src/Setup.sh

@@ -37,14 +37,29 @@ then
     esac
 fi
 
+# Then, check if the ftp container is already running.
+if [[ $(docker inspect -f '{{.State.Running}}' $DOCKER_FTP_TAG) == "true" ]]
+then
+    printf "%s\n" "$DOCKER_FTP_TAG is currently running."
+    printf "%s\n" "The container must be stopped before rebuilding any images."
+    printf "%s\n" "Would you like to proceed? (Y/N)"
+    read -p ">" choice
+    case "$choice" in
+        Y|y ) docker stop $DOCKER_FTP_TAG;;
+        * ) exit 0;;
+    esac
+fi
+
 # remove old containers
 docker container rm --force $DOCKER_ALASKA_TAG
 docker container rm --force $DOCKER_CGI_TAG
+docker container rm --force $DOCKER_FTP_TAG
 
 # make data volumes
 docker volume create --name $DOCKER_SCRIPT_VOLUME
 docker volume create --name $DOCKER_DATA_VOLUME
 docker volume create --name $DOCKER_CGI_VOLUME
+docker volume create --name $DOCKER_FTP_VOLUME
 
 # build alaska image
 Docker/alaska/build_image.sh
@@ -109,3 +124,11 @@ if [ $exit_code -ne 0 ]; then
     printf "%s\n" "Failed to build $DOCKER_CGI_TAG container."
     exit $exit_code
 fi
+
+# ftp container
+Docker/ftp/build_container.sh
+exit_code=$?
+if [ $exit_code -ne 0 ]; then
+    printf "%s\n" "Failed to build $DOCKER_FTP_TAG container."
+    exit $exit_code
+fi

src/scripts/set_env_variables.sh

@@ -3,6 +3,9 @@
 # These include: Update.sh, Setup.sh, and Start.sh
 # This script is to be called with the 'source' prefix.
 
+# Timezone for all containers.
+TIMEZONE="America/Los_Angeles"
+
 ####### DEFINE VARIABLES #######
 # Docker tags.
 DOCKER_SCRIPT_VOLUME="alaska_script_volume"
@@ -24,21 +27,19 @@ DOCKER_SOCKET_MOUNT="/var/run/docker.sock:/var/run/docker.sock"
 DOCKER_SCRIPT_MOUNT="$DOCKER_SCRIPT_VOLUME:/alaska/scripts"
 DOCKER_DATA_MOUNT="$DOCKER_DATA_VOLUME:/alaska/root"
 DOCKER_CGI_MOUNT="$DOCKER_CGI_VOLUME:/usr/lib/cgi-bin/alaska"
-# DOCKER_FTP_MOUNT="$DOCKER_FTP_VOLUME:/etc/pure-ftpd"
-DOCKER_FTP_MOUNT="ftppswd:/etc/pure-ftpd"
+DOCKER_FTP_MOUNT="$DOCKER_FTP_VOLUME:/etc/pure-ftpd"
+# DOCKER_FTP_MOUNT="ftppswd:/etc/pure-ftpd"
 
 # Port mappings & networking.
 DOCKER_CGI_PORT="80:80"
 DOCKER_FTP_PORT="21:21"
 DOCKER_FTP_PORTS="30000-30009:30000-30009"
-DOCKER_FTP_ENV1="PUBLICHOST=bagua.caltech.edu"
-DOCKER_FTP_ENV2="ADDED_FLAGS=-d -d"
-DOCKER_FTP_ENV3="ADDED_FLAGS=-O w3c:/var/log/pure-ftpd/transfer.log"
+DOCKER_FTP_HOST="PUBLICHOST=alaska.caltech.edu"
+DOCKER_FTP_FLAGS="ADDED_FLAGS=-d -d -O w3c:/var/log/pure-ftpd/transfer.log -c 25 -C 10"
 
 # Declare array varables for required images, containers, volumes, and networks
 declare -a images=(
     "$DOCKER_ALASKA_TAG"
-    "$DOCKER_FTP_TAG"
     "$DOCKER_REQUEST_TAG"
     "$DOCKER_QC_TAG"
     "$DOCKER_KALLISTO_TAG"