--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/docker/startup.sh	Sun Aug 16 08:11:10 2020 -0400
@@ -0,0 +1,462 @@
+#!/usr/bin/env bash
+
+# Migration path for old images that had the tool_deps under /export/galaxy-central/tool_deps/
+
+if [ -d "/export/galaxy-central/tool_deps/" ] && [ ! -L "/export/galaxy-central/tool_deps/" ]; then
+    mkdir -p /export/tool_deps/
+    mv /export/galaxy-central/tool_deps /export/
+    ln -s /export/tool_deps/ $GALAXY_ROOT/
+fi
+
+# This is needed for Docker compose to have a unified alias for the main container.
+# Modifying /etc/hosts can only happen during runtime not during build-time
+echo "127.0.0.1      galaxy" >> /etc/hosts
+
+# Set number of Galaxy handlers via GALAXY_HANDLER_NUMPROCS or default to 2
+ansible localhost -m ini_file -a "dest=/etc/supervisor/conf.d/galaxy.conf section=program:handler option=numprocs value=${GALAXY_HANDLER_NUMPROCS:-2}" &> /dev/null
+
+# If the Galaxy config file is not in the expected place, copy from the sample
+# and hope for the best (that the admin has done all the setup through env vars.)
+if [ ! -f $GALAXY_CONFIG_FILE ]
+  then
+  # this should succesfully copy either .yml or .ini sample file to the expected location
+  cp /export/config/galaxy${GALAXY_CONFIG_FILE: -4}.sample $GALAXY_CONFIG_FILE
+fi
+
+# Configure proxy prefix filtering
+if [[ ! -z $PROXY_PREFIX ]]
+    then
+    if [ ${GALAXY_CONFIG_FILE: -4} == ".ini" ]
+        then
+        ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_FILE} section=filter:proxy-prefix option=prefix value=${PROXY_PREFIX}" &> /dev/null
+        ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_FILE} section=app:main option=filter-with value=proxy-prefix" &> /dev/null
+    else
+        ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^  module:' state=absent" &> /dev/null
+        ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^  socket:' state=absent" &> /dev/null
+        ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^  mount:' state=absent" &> /dev/null
+        ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^  manage-script-name:' state=absent" &> /dev/null
+        ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line='  manage-script-name: true'" &> /dev/null
+        ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line='  mount: ${PROXY_PREFIX}=galaxy.webapps.galaxy.buildapp:uwsgi_app()'" &> /dev/null
+        ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line='  socket: unix:///srv/galaxy/var/uwsgi.sock'" &> /dev/null
+
+        # Also set SCRIPT_NAME. It's not always necessary due to manage-script-name: true in galaxy.yml, but it makes life easier in this container + it does no harm
+        ansible localhost -m lineinfile -a "path=/etc/nginx/conf.d/uwsgi.conf regexp='^    uwsgi_param SCRIPT_NAME' state=absent" &> /dev/null
+        ansible localhost -m lineinfile -a "path=/etc/nginx/conf.d/uwsgi.conf insertafter='^    include uwsgi_params' line='    uwsgi_param SCRIPT_NAME ${PROXY_PREFIX};'" &> /dev/null
+    fi
+
+    ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_DIR}/reports_wsgi.ini section=filter:proxy-prefix option=prefix value=${PROXY_PREFIX}/reports" &> /dev/null
+    ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_DIR}/reports_wsgi.ini section=app:main option=filter-with value=proxy-prefix" &> /dev/null
+
+    # Fix path to html assets
+    ansible localhost -m replace -a "dest=$GALAXY_CONFIG_DIR/web/welcome.html regexp='(href=\"|\')[/\\w]*(/static)' replace='\\1${PROXY_PREFIX}\\2'" &> /dev/null
+
+    # Set some other vars based on that prefix
+    if [ "x$GALAXY_CONFIG_COOKIE_PATH" == "x" ]
+        then
+        export GALAXY_CONFIG_COOKIE_PATH="$PROXY_PREFIX"
+    fi
+    if [ "x$GALAXY_CONFIG_DYNAMIC_PROXY_PREFIX" == "x" ]
+        then
+        export GALAXY_CONFIG_DYNAMIC_PROXY_PREFIX="$PROXY_PREFIX/gie_proxy"
+    fi
+
+    # Change the defaults nginx upload/x-accel paths
+    if [ "$GALAXY_CONFIG_NGINX_UPLOAD_PATH" == "/_upload" ]
+        then
+            export GALAXY_CONFIG_NGINX_UPLOAD_PATH="${PROXY_PREFIX}${GALAXY_CONFIG_NGINX_UPLOAD_PATH}"
+    fi
+fi
+
+# Disable authentication of Galaxy reports
+if [[ ! -z $DISABLE_REPORTS_AUTH ]]
+    then
+        # disable authentification
+        echo "Disable Galaxy reports authentification "
+        echo "" > /etc/nginx/conf.d/reports_auth.conf
+    else
+        # enable authentification
+        echo "Enable Galaxy reports authentification "
+        cp /etc/nginx/conf.d/reports_auth.conf.source /etc/nginx/conf.d/reports_auth.conf
+fi
+
+# Try to guess if we are running under --privileged mode
+if [[ ! -z $HOST_DOCKER_LEGACY ]]; then
+    if mount | grep "/proc/kcore"; then
+        PRIVILEGED=false
+    else
+        PRIVILEGED=true
+    fi
+else
+    # Taken from http://stackoverflow.com/questions/32144575/how-to-know-if-a-docker-container-is-running-in-privileged-mode
+    ip link add dummy0 type dummy 2>/dev/null
+    if [[ $? -eq 0 ]]; then
+        PRIVILEGED=true
+        # clean the dummy0 link
+        ip link delete dummy0 2>/dev/null
+    else
+        PRIVILEGED=false
+    fi
+fi
+
+cd $GALAXY_ROOT
+. $GALAXY_VIRTUAL_ENV/bin/activate
+
+if $PRIVILEGED; then
+    umount /var/lib/docker
+fi
+
+if [[ ! -z $STARTUP_EXPORT_USER_FILES ]]; then
+    # If /export/ is mounted, export_user_files file moving all data to /export/
+    # symlinks will point from the original location to the new path under /export/
+    # If /export/ is not given, nothing will happen in that step
+    echo "Checking /export..."
+    python3 /usr/local/bin/export_user_files.py $PG_DATA_DIR_DEFAULT
+fi
+
+# Delete compiled templates in case they are out of date
+if [[ ! -z $GALAXY_CONFIG_TEMPLATE_CACHE_PATH ]]; then
+    rm -rf $GALAXY_CONFIG_TEMPLATE_CACHE_PATH/*
+fi
+
+# Enable loading of dependencies on startup. Such as LDAP.
+# Adapted from galaxyproject/galaxy/scripts/common_startup.sh
+if [[ ! -z $LOAD_GALAXY_CONDITIONAL_DEPENDENCIES ]]
+    then
+        echo "Installing optional dependencies in galaxy virtual environment..."
+        : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"}
+        GALAXY_CONDITIONAL_DEPENDENCIES=$(PYTHONPATH=lib python -c "import galaxy.dependencies; print('\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE')))")
+        [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -q -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}"
+fi
+
+if [[ ! -z $LOAD_GALAXY_CONDITIONAL_DEPENDENCIES ]] && [[ ! -z $LOAD_PYTHON_DEV_DEPENDENCIES ]]
+    then
+        echo "Installing development requirements in galaxy virtual environment..."
+        : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"}
+        dev_requirements='./lib/galaxy/dependencies/dev-requirements.txt'
+        [ -f $dev_requirements ] && pip install -q -r $dev_requirements --index-url "${GALAXY_WHEELS_INDEX_URL}"
+fi
+
+# Enable Test Tool Shed
+if [[ ! -z $ENABLE_TTS_INSTALL ]]
+    then
+        echo "Enable installation from the Test Tool Shed."
+        export GALAXY_CONFIG_TOOL_SHEDS_CONFIG_FILE=$GALAXY_HOME/tool_sheds_conf.xml
+fi
+
+# Remove all default tools from Galaxy by default
+if [[ ! -z $BARE ]]
+    then
+        echo "Remove all tools from the tool_conf.xml file."
+        export GALAXY_CONFIG_TOOL_CONFIG_FILE=config/shed_tool_conf.xml,$GALAXY_ROOT/test/functional/tools/upload_tool_conf.xml
+fi
+
+# If auto installing conda envs, make sure bcftools is installed for __set_metadata__ tool
+if [[ ! -z $GALAXY_CONFIG_CONDA_AUTO_INSTALL ]]
+    then
+        if [ ! -d "/tool_deps/_conda/envs/__bcftools@1.5" ]; then
+            su $GALAXY_USER -c "/tool_deps/_conda/bin/conda create -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __bcftools@1.5 bcftools=1.5"
+            su $GALAXY_USER -c "/tool_deps/_conda/bin/conda clean --tarballs --yes"
+        fi
+fi
+
+if [[ ! -z $GALAXY_EXTRAS_CONFIG_POSTGRES ]]; then
+    if [[ $NONUSE != *"postgres"* ]]
+    then
+        # Backward compatibility for exported postgresql directories before version 15.08.
+        # In previous versions postgres has the UID/GID of 102/106. We changed this in
+        # https://github.com/bgruening/docker-galaxy-stable/pull/71 to GALAXY_POSTGRES_UID=1550 and
+        # GALAXY_POSTGRES_GID=1550
+        if [ -e /export/postgresql/ ];
+            then
+                if [ `stat -c %g /export/postgresql/` == "106" ];
+                    then
+                        chown -R postgres:postgres /export/postgresql/
+                fi
+        fi
+    fi
+fi
+
+
+if [[ ! -z $GALAXY_EXTRAS_CONFIG_CONDOR ]]; then
+    if [[ ! -z $ENABLE_CONDOR ]]
+    then
+        if [[ ! -z $CONDOR_HOST ]]
+        then
+            echo "Enabling Condor with external scheduler at $CONDOR_HOST"
+        echo "# Config generated by startup.sh
+CONDOR_HOST = $CONDOR_HOST
+ALLOW_ADMINISTRATOR = *
+ALLOW_OWNER = *
+ALLOW_READ = *
+ALLOW_WRITE = *
+ALLOW_CLIENT = *
+ALLOW_NEGOTIATOR = *
+DAEMON_LIST = MASTER, SCHEDD
+UID_DOMAIN = galaxy
+DISCARD_SESSION_KEYRING_ON_STARTUP = False
+TRUST_UID_DOMAIN = true" > /etc/condor/condor_config.local
+        fi
+
+        if [[ -e /export/condor_config ]]
+        then
+            echo "Replacing Condor config by locally supplied config from /export/condor_config"
+            rm -f /etc/condor/condor_config
+            ln -s /export/condor_config /etc/condor/condor_config
+        fi
+    fi
+fi
+
+
+# Copy or link the slurm/munge config files
+if [ -e /export/slurm.conf ]
+then
+    rm -f /etc/slurm-llnl/slurm.conf
+    ln -s /export/slurm.conf /etc/slurm-llnl/slurm.conf
+else
+    # Configure SLURM with runtime hostname.
+    # Use absolute path to python so virtualenv is not used.
+    /usr/bin/python /usr/sbin/configure_slurm.py
+fi
+if [ -e /export/munge.key ]
+then
+    rm -f /etc/munge/munge.key
+    ln -s /export/munge.key /etc/munge/munge.key
+    chmod 400 /export/munge.key
+fi
+
+# link the gridengine config file
+if [ -e /export/act_qmaster ]
+then
+    rm -f /var/lib/gridengine/default/common/act_qmaster
+    ln -s /export/act_qmaster /var/lib/gridengine/default/common/act_qmaster
+fi
+
+# Waits until postgres is ready
+function wait_for_postgres {
+    echo "Checking if database is up and running"
+    until /usr/local/bin/check_database.py 2>&1 >/dev/null; do sleep 1; echo "Waiting for database"; done
+    echo "Database connected"
+}
+
+# $NONUSE can be set to include cron, proftp, reports or nodejs
+# if included we will _not_ start these services.
+function start_supervisor {
+    supervisord -c /etc/supervisor/supervisord.conf
+    sleep 5
+
+    if [[ ! -z $SUPERVISOR_MANAGE_POSTGRES && ! -z $SUPERVISOR_POSTGRES_AUTOSTART ]]; then
+        if [[ $NONUSE != *"postgres"* ]]
+        then
+            echo "Starting postgres"
+            supervisorctl start postgresql
+        fi
+    fi
+
+    wait_for_postgres
+
+    # Make sure the database is automatically updated
+    if [[ ! -z $GALAXY_AUTO_UPDATE_DB ]]
+    then
+        echo "Updating Galaxy database"
+        sh manage_db.sh -c /etc/galaxy/galaxy.yml upgrade
+    fi
+
+    if [[ ! -z $SUPERVISOR_MANAGE_CRON ]]; then
+        if [[ $NONUSE != *"cron"* ]]
+        then
+            echo "Starting cron"
+            supervisorctl start cron
+        fi
+    fi
+
+    if [[ ! -z $SUPERVISOR_MANAGE_PROFTP ]]; then
+        if [[ $NONUSE != *"proftp"* ]]
+        then
+            echo "Starting ProFTP"
+            supervisorctl start proftpd
+        fi
+    fi
+
+    if [[ ! -z $SUPERVISOR_MANAGE_REPORTS ]]; then
+        if [[ $NONUSE != *"reports"* ]]
+        then
+            echo "Starting Galaxy reports webapp"
+            supervisorctl start reports
+        fi
+    fi
+
+    if [[ ! -z $SUPERVISOR_MANAGE_IE_PROXY ]]; then
+        if [[ $NONUSE != *"nodejs"* ]]
+        then
+            echo "Starting nodejs"
+            supervisorctl start galaxy:galaxy_nodejs_proxy
+        fi
+    fi
+
+    if [[ ! -z $SUPERVISOR_MANAGE_CONDOR ]]; then
+        if [[ $NONUSE != *"condor"* ]]
+        then
+            echo "Starting condor"
+            supervisorctl start condor
+        fi
+    fi
+
+    if [[ ! -z $SUPERVISOR_MANAGE_SLURM ]]; then
+        if [[ $NONUSE != *"slurmctld"* ]]
+        then
+            echo "Starting slurmctld"
+            supervisorctl start slurmctld
+        fi
+        if [[ $NONUSE != *"slurmd"* ]]
+        then
+            echo "Starting slurmd"
+            supervisorctl start slurmd
+        fi
+        supervisorctl start munge
+    else
+        if [[ $NONUSE != *"slurmctld"* ]]
+        then
+            echo "Starting slurmctld"
+            /usr/sbin/slurmctld -L $GALAXY_LOGS_DIR/slurmctld.log
+        fi
+        if [[ $NONUSE != *"slurmd"* ]]
+        then
+            echo "Starting slurmd"
+            /usr/sbin/slurmd -L $GALAXY_LOGS_DIR/slurmd.log
+        fi
+
+        # We need to run munged regardless
+        mkdir -p /var/run/munge && /usr/sbin/munged -f
+    fi
+}
+
+if [[ ! -z $SUPERVISOR_POSTGRES_AUTOSTART ]]; then
+    if [[ $NONUSE != *"postgres"* ]]
+    then
+        # Change the data_directory of postgresql in the main config file
+        ansible localhost -m lineinfile -a "line='data_directory = \'$PG_DATA_DIR_HOST\'' dest=$PG_CONF_DIR_DEFAULT/postgresql.conf backup=yes state=present regexp='data_directory'" &> /dev/null
+    fi
+fi
+
+if $PRIVILEGED; then
+    echo "Enable Galaxy Interactive Environments."
+    export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY="config/plugins/interactive_environments"
+    if [ x$DOCKER_PARENT == "x" ]; then
+        #build the docker in docker environment
+        bash /root/cgroupfs_mount.sh
+        start_supervisor
+        supervisorctl start docker
+    else
+        #inheriting /var/run/docker.sock from parent, assume that you need to
+        #run docker with sudo to validate
+        echo "$GALAXY_USER ALL = NOPASSWD : ALL" >> /etc/sudoers
+        start_supervisor
+    fi
+    if  [[ ! -z $PULL_IE_IMAGES ]]; then
+        echo "About to pull IE images. Depending on the size, this may take a while!"
+
+        for ie in {JUPYTER,RSTUDIO,ETHERCALC,PHINCH,NEO}; do
+            enabled_var_name="GALAXY_EXTRAS_IE_FETCH_${ie}";
+            if [[ ${!enabled_var_name} ]]; then
+                # Store name in a var
+                image_var_name="GALAXY_EXTRAS_${ie}_IMAGE"
+                # And then read from that var
+                docker pull "${!image_var_name}"
+            fi
+        done
+    fi
+
+    # in privileged mode autofs and CVMFS is available
+    # install autofs
+    echo "Installing autofs to enable automatic CVMFS mounts"
+    apt-get install autofs --no-install-recommends -y
+    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/*
+else
+    echo "Disable Galaxy Interactive Environments. Start with --privileged to enable IE's."
+    export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY=""
+    start_supervisor
+fi
+
+if [ "$USE_HTTPS_LETSENCRYPT" != "False" ]
+then
+    echo "Settting up letsencrypt"
+    ansible-playbook -c local /ansible/provision.yml \
+    --extra-vars gather_facts=False \
+    --extra-vars galaxy_extras_config_ssl=True \
+    --extra-vars galaxy_extras_config_ssl_method=letsencrypt \
+    --extra-vars galaxy_extras_galaxy_domain="GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL" \
+    --extra-vars galaxy_extras_config_nginx_upload=False \
+    --tags https
+fi
+if [ "$USE_HTTPS" != "False" ]
+then
+    if [ -f /export/server.key -a -f /export/server.crt ]
+    then
+        echo "Copying SSL keys"
+        ansible-playbook -c local /ansible/provision.yml \
+        --extra-vars gather_facts=False \
+        --extra-vars galaxy_extras_config_ssl=True \
+        --extra-vars galaxy_extras_config_ssl_method=own \
+        --extra-vars src_nginx_ssl_certificate_key=/export/server.key \
+        --extra-vars src_nginx_ssl_certificate=/export/server.crt \
+        --extra-vars galaxy_extras_config_nginx_upload=False \
+        --tags https
+    else
+        echo "Setting up self-signed SSL keys"
+        ansible-playbook -c local /ansible/provision.yml \
+        --extra-vars gather_facts=False \
+        --extra-vars galaxy_extras_config_ssl=True \
+        --extra-vars galaxy_extras_config_ssl_method=self-signed \
+        --extra-vars galaxy_extras_config_nginx_upload=False \
+        --tags https
+    fi
+fi
+
+# In case the user wants the default admin to be created, do so.
+if [[ ! -z $GALAXY_DEFAULT_ADMIN_USER ]]
+    then
+        echo "Creating admin user $GALAXY_DEFAULT_ADMIN_USER with key $GALAXY_DEFAULT_ADMIN_KEY and password $GALAXY_DEFAULT_ADMIN_PASSWORD if not existing"
+        python /usr/local/bin/create_galaxy_user.py --user "$GALAXY_DEFAULT_ADMIN_EMAIL" --password "$GALAXY_DEFAULT_ADMIN_PASSWORD" \
+        -c "$GALAXY_CONFIG_FILE" --username "$GALAXY_DEFAULT_ADMIN_USER" --key "$GALAXY_DEFAULT_ADMIN_KEY"
+fi
+# If there is a need to execute actions that would require a live galaxy instance, such as adding workflows, setting quotas, adding more users, etc.
+# then place a file with that logic named post-start-actions.sh on the /export/ directory, it should have access to all environment variables
+# visible here.
+# The file needs to be executable (chmod a+x post-start-actions.sh)
+# uses ephemeris, present in docker-galaxy-stable, to wait for the local instance
+
+if [[ -f /export/post-start-actions.sh ]] 
+    then 
+       /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > $GALAXY_LOGS_DIR/post-start-actions.log
+       /export/post-start-actions.sh >> $GALAXY_LOGS_DIR/post-start-actions.log &
+    else
+       echo "No /export/post-start-actions.sh found or not executable so not running" >> $GALAXY_LOGS_DIR/post-start-actions.log
+fi
+
+
+# Reinstall tools if the user want to
+if [[ ! -z $GALAXY_AUTO_UPDATE_TOOLS ]]
+    then
+        /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > /home/galaxy/logs/post-start-actions.log &&
+        OLDIFS=$IFS
+        IFS=','
+        for TOOL_YML in `echo "$GALAXY_AUTO_UPDATE_TOOLS"`
+        do
+            echo "Installing tools from $TOOL_YML"
+            /tool_deps/_conda/bin/shed-tools install -g "http://127.0.0.1" -a "$GALAXY_DEFAULT_ADMIN_KEY" -t "$TOOL_YML"
+            /tool_deps/_conda/bin/conda clean --tarballs --yes
+        done
+        IFS=$OLDIFS
+fi
+
+# migrate custom IEs or Visualisations (Galaxy plugins)
+# this is needed for by the new client build system
+python3 ${GALAXY_ROOT}/scripts/plugin_staging.py
+
+# Enable verbose output
+if [ `echo ${GALAXY_LOGGING:-'no'} | tr [:upper:] [:lower:]` = "full" ]
+    then
+        tail -f /var/log/supervisor/* /var/log/nginx/* $GALAXY_LOGS_DIR/*.log
+    else
+        tail -f $GALAXY_LOGS_DIR/*.log
+fi