fix

Dockerfile

-FROM php:apache
+FROM php:7.2-apache
+
+# Install packages and PHP-extensions
+RUN apt-get -q update && \
+    mkdir -p /usr/share/man/man1 /usr/share/man/man7 && \
+    DEBIAN_FRONTEND=noninteractive apt-get -yq --no-install-recommends install \
+    file libfreetype6 libjpeg62 libpng16-16 libpq-dev libx11-6 libxpm4 \
+    postgresql-client wget patch cron logrotate git nano python python-requests python-setuptools \
+    memcached libmemcached11 libmemcachedutil2 gpg dirmngr ca-certificates && \
+    BUILD_DEPS="libfreetype6-dev libjpeg62-turbo-dev libmcrypt-dev libpng-dev libxpm-dev re2c zlib1g-dev libmemcached-dev python-pip python-dev libpq-dev"; \
+    DEBIAN_FRONTEND=noninteractive apt-get -yq --no-install-recommends install $BUILD_DEPS \
+ && docker-php-ext-configure gd \
+        --with-jpeg-dir=/usr/lib/x86_64-linux-gnu --with-png-dir=/usr/lib/x86_64-linux-gnu \
+        --with-xpm-dir=/usr/lib/x86_64-linux-gnu --with-freetype-dir=/usr/lib/x86_64-linux-gnu \
+ && docker-php-ext-install gd mbstring pdo_pgsql zip \
+ && pip install chado==2.1.1 tripal==3.0 \
+ && pecl install memcached \
+ && apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false -o APT::AutoRemove::SuggestsImportant=false $BUILD_DEPS \
+ && rm -rf /var/lib/apt/lists/*
+# && pecl install uploadprogress # not yet compatible with php7 on PECL
 
 ENV TINI_VERSION v0.9.0
 RUN set -x \
     && curl -fSL "https://github.com/krallin/tini/releases/download/$TINI_VERSION/tini" -o /usr/local/bin/tini \
     && curl -fSL "https://github.com/krallin/tini/releases/download/$TINI_VERSION/tini.asc" -o /usr/local/bin/tini.asc \
     && export GNUPGHOME="$(mktemp -d)" \
-    && gpg --keyserver ha.pool.sks-keyservers.net --recv-keys 6380DC428747F6C393FEACA59A84159D7001A4E5 \
+    && gpg --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys 6380DC428747F6C393FEACA59A84159D7001A4E5 \
+    || gpg --keyserver pgp.mit.edu --recv-keys 6380DC428747F6C393FEACA59A84159D7001A4E5 \
     && gpg --batch --verify /usr/local/bin/tini.asc /usr/local/bin/tini \
-    && rm -r "$GNUPGHOME" /usr/local/bin/tini.asc \
+    && rm -rf "$GNUPGHOME" /usr/local/bin/tini.asc \
     && chmod +x /usr/local/bin/tini
 
 ENTRYPOINT ["/usr/local/bin/tini", "--"]
@@ -17,28 +37,12 @@ RUN ln -s /var/www/html /app
 # Update apache2 configuration for drupal
 RUN a2enmod rewrite && a2enmod proxy && a2enmod proxy_http
 
-# Install packages and PHP-extensions
-RUN apt-get -q update && \
-    DEBIAN_FRONTEND=noninteractive apt-get -yq --no-install-recommends install \
-    file libfreetype6 libjpeg62 libpng12-0 libpq-dev libx11-6 libxpm4 \
-    postgresql-client wget patch cron logrotate git python python-requests && \
-    BUILD_DEPS="libfreetype6-dev libjpeg62-turbo-dev libmcrypt-dev libpng12-dev libxpm-dev re2c zlib1g-dev python-pip python-dev libpq-dev"; \
-    DEBIAN_FRONTEND=noninteractive apt-get -yq --no-install-recommends install $BUILD_DEPS \
- && docker-php-ext-configure gd \
-        --with-jpeg-dir=/usr/lib/x86_64-linux-gnu --with-png-dir=/usr/lib/x86_64-linux-gnu \
-        --with-xpm-dir=/usr/lib/x86_64-linux-gnu --with-freetype-dir=/usr/lib/x86_64-linux-gnu \
- && docker-php-ext-install gd mbstring pdo_pgsql zip \
- && pip install chado tripal \
- && apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false -o APT::AutoRemove::SuggestsImportant=false $BUILD_DEPS \
- && rm -rf /var/lib/apt/lists/*
-# && pecl install uploadprogress # not yet compatible with php7 on PECL
-
 # Compile a php7 compatible version of uploadprogress module
 RUN cd /tmp && git clone https://github.com/php/pecl-php-uploadprogress.git && cd pecl-php-uploadprogress && phpize && ./configure && make && make install && cd /
 
 # Download Drupal from ftp.drupal.org
-ENV DRUPAL_VERSION=7.53
-ENV DRUPAL_TARBALL_MD5=4230279ecca4f0cde652a219e10327e7
+ENV DRUPAL_VERSION=7.59
+ENV DRUPAL_TARBALL_MD5=7e09c6b177345a81439fe0aa9a2d15fc
 WORKDIR /var/www
 RUN rm -R html \
  && curl -OsS https://ftp.drupal.org/files/projects/drupal-${DRUPAL_VERSION}.tar.gz \
@@ -55,7 +59,56 @@ RUN curl -sS https://getcomposer.org/installer | php -- --install-dir=/usr/local
  && drush cc drush \
  && mkdir /etc/drush && echo "<?php\n\$options['yes'] = TRUE;\n\$options['v'] = TRUE;\n" > /etc/drush/drushrc.php
 
-RUN wget https://github.com/erasche/chado-schema-builder/releases/download/1.31-jenkins90/chado-1.31-tripal.sql.gz -O /chado-master-tripal.sql.gz
+RUN wget https://github.com/erasche/chado-schema-builder/releases/download/1.31-jenkins110/chado-1.31-tripal.sql.gz -O /chado-master-tripal.sql.gz \
+    && wget --no-check-certificate https://drupal.org/files/drupal.pgsql-bytea.27.patch -O /drupal.pgsql-bytea.27.patch
+
+WORKDIR html
+
+# Install elasticsearch php library (required by tripal_elasticsearch)
+RUN cd /var/www/html/sites/all/libraries/\
+    && mkdir elasticsearch-php \
+    && cd elasticsearch-php \
+    && composer require "elasticsearch/elasticsearch:~5.0" \
+    && cd /var/www/html/
+
+ENV BASE_URL_PATH="/tripal" \
+    GALAXY_SHARED_DIR="/tripal-data/" \
+    ENABLE_DRUPAL_CACHE=1 \
+    ENABLE_OP_CACHE=1 \
+    ENABLE_MEMCACHE=1 \
+    ENABLE_CRON_JOBS=0 \
+    TRIPAL_BASE_CODE_GIT="https://github.com/tripal/tripal.git[@01c1f154b3fb27fa822d24546d0c7ed76ccf4cc6]" \
+    TRIPAL_GIT_CLONE_MODULES="https://github.com/abretaud/tripal_rest_api.git[@cb1d52ffed0b8a5c1ac189b41c729c8ad93b1c21] https://github.com/tripal/tripal_elasticsearch.git[@bac9c5d35f4c38e906fe48f55064906af8ea029a] https://github.com/tripal/trpdownload_api.git" \
+    TRIPAL_DOWNLOAD_MODULES="queue_ui tripal_analysis_interpro-7.x-2.x-dev tripal_analysis_blast-7.x-2.x-dev tripal_analysis_go-7.x-2.x-dev" \
+    TRIPAL_ENABLE_MODULES="tripal_genetic tripal_natural_diversity tripal_phenotype tripal_project tripal_pub tripal_stock tripal_analysis_blast tripal_analysis_interpro tripal_analysis_go tripal_rest_api tripal_elasticsearch trpdownload_api"
+
+RUN repo_url=`echo $TRIPAL_BASE_CODE_GIT | sed 's/\(.\+\)\[@\w\+\]/\1/'`; \
+    rev=`echo $TRIPAL_BASE_CODE_GIT | sed 's/.\+\[@\(\w\+\)\]/\1/'`; \
+    git clone $repo_url /var/www/html/sites/all/modules/tripal; \
+    if [ "$repo_url" != "$rev" ]; then \
+        cd /var/www/html/sites/all/modules/tripal; \
+        git reset --hard $rev; \
+        cd /var/www/html/; \
+    fi;
+
+# Pre download all default modules
+RUN drush pm-download ctools views libraries services ultimate_cron memcache ${TRIPAL_BASE_MODULE} \
+    $TRIPAL_DOWNLOAD_MODULES \
+    && for repo in $TRIPAL_GIT_CLONE_MODULES; do \
+        repo_url=`echo $repo | sed 's/\(.\+\)\[@\w\+\]/\1/'`; \
+        rev=`echo $repo | sed 's/.\+\[@\(\w\+\)\]/\1/'`; \
+        module_name=`basename $repo_url .git`; \
+        git clone $repo_url /var/www/html/sites/all/modules/$module_name; \
+        if [ "$repo_url" != "$rev" ]; then \
+            cd /var/www/html/sites/all/modules/$module_name; \
+            git reset --hard $rev; \
+            cd /var/www/html/sites/all/modules/; \
+        fi; \
+    done
+
+RUN cd /var/www/html/sites/all/modules/views \
+    && patch -p1 < ../tripal/tripal_views/views-sql-compliant-three-tier-naming-1971160-30.patch \
+    && cd /var/www/html/
 
 # Add custom functions
 ADD search.sql /search.sql
@@ -67,7 +120,6 @@ ADD php-conf.d/ $PHP_INI_DIR/conf.d/
 ADD logrotate.d/tripal /etc/logrotate.d/
 
 # copy sites/default's defaults
-WORKDIR html
 ADD etc/tripal/settings.php /etc/tripal/settings.php
 
 # Add README.md, entrypoint-script and scripts-folder
@@ -76,11 +128,4 @@ ADD /scripts/ /scripts/
 
 ADD tripal_apache.conf /etc/apache2/conf-enabled/tripal_apache.conf
 
-ENV BASE_URL_PATH="/tripal" \
-    ENABLE_DRUPAL_CACHE=1 \
-    ENABLE_OP_CACHE=1\
-    TRIPAL_GIT_CLONE_MODULES="https://github.com/abretaud/tripal_rest_api.git https://github.com/tripal/tripal_elasticsearch.git" \
-    TRIPAL_DOWNLOAD_MODULES="tripal_analysis_interpro-7.x-2.x-dev tripal_analysis_blast-7.x-2.x-dev tripal_analysis_go-7.x-2.x-dev" \
-    TRIPAL_ENABLE_MODULES="tripal_genetic tripal_natural_diversity tripal_phenotype tripal_project tripal_pub tripal_stock tripal_analysis_blast tripal_analysis_interpro tripal_analysis_go tripal_rest_api tripal_elasticsearch"
-
 CMD ["/entrypoint.sh"]

README.md

 # Tripal Docker Image
 
+[![Docker Automated build](https://img.shields.io/docker/automated/erasche/tripal.svg?style=flat-square)](https://hub.docker.com/r/erasche/tripal/)
 [![DOI](https://zenodo.org/badge/10899/erasche/docker-tripal.svg)](https://zenodo.org/badge/latestdoi/10899/erasche/docker-tripal)
 
 ![Tripal Logo](http://tripal.info/sites/default/files/TripalLogo_dark.png)
 
-This image contains a ready-to-go installation of Tripal v2.1.
+This image contains a ready-to-go installation of Tripal v2.x.
 
 ## Using the Container
 
@@ -40,7 +41,7 @@ services:
     ports:
       - "3000:80"
   db:
-    image: erasche/chado:1.31-jenkins97-pg9.5
+    image: erasche/chado
     environment:
       - POSTGRES_PASSWORD=postgres
         # The default chado image would try to install the schema on first run,
@@ -88,8 +89,12 @@ By default some caching is done for better performances. You can disable it with
 ```
 ENABLE_OP_CACHE: 0 # To disable the PHP opcache
 ENABLE_DRUPAL_CACHE: 0 # To disable Drupal built-in cache
+ENABLE_MEMCACHE: 0 # To disable caching using memcache (requires ENABLE_DRUPAL_CACHE=1)
 ```
 
+If ENABLE_DRUPAL_CACHE is enabled but ENABLE_MEMCACHE is not, Drupal will cache data into database.
+If both ENABLE_DRUPAL_CACHE and ENABLE_MEMCACHE are enabled, Drupal will cache data using memcache.
+
 ## Customizing the Image
 
 To build a derivative image from this, it should be as simple as writing a Dockerfile which builds off of this image.
@@ -111,10 +116,45 @@ If you need to install a module that is not hosted on http://www.drupal.org, you
 ENV TRIPAL_GIT_CLONE_MODULES="https://github.com/abretaud/tripal_rest_api.git https://github.com/tripal/tripal_analysis_expression.git"
 ```
 
-## Tripal usage
+If you want to get a specific git revision, you can use this syntax:
+
+```
+ENV TRIPAL_GIT_CLONE_MODULES="https://github.com/abretaud/tripal_rest_api.git[@cb1d52ffed0b8a5c1ac189b41c729c8ad93b1c21]"
+```
+
+## Tripal jobs
+
+When loading data into Tripal, jobs or indexing tasks will be created inside the container.
+
+If you are using [Tripaille](https://github.com/abretaud/python-tripal) to load data, you have nothing specific to do, jobs will be launched automatically for you.
+
+If you don't use Tripaille, you will need to manually launch Tripal jobs or indexing tasks, as described in the Tripal documentation:
+
+```
+# Launch all jobs in queue
+docker-compose exec web "drush trp-run-jobs --username=admin"
+
+# Launch indexing tasks in all queues
+docker-compose exec web "export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_0"
+docker-compose exec web "export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_1"
+docker-compose exec web "export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_2"
+docker-compose exec web "export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_3"
+docker-compose exec web "export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_4"
+docker-compose exec web "export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_5"
+docker-compose exec web "export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_6"
+docker-compose exec web "export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_7"
+docker-compose exec web "export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_8"
+docker-compose exec web "export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_9"
+```
+
+The container can also be configured to launch Tripal jobs automatically every 2 minutes using cron:
+
+```
+ENABLE_CRON_JOBS=1
+```
 
-The container is configured (with cron) to launch Tripal jobs in queue every 2 minutes.
-The log of these jobs is available in the /var/log/tripal_jobs.log log file, which is emptied regularly.
+The downside of this option is that cron will coninue to launch processes every 2 minutes, even when no jobs are scheduled, leading to a little more cpu usage every 2 minutes.
+The log of these jobs will be available in the /var/log/tripal_jobs.log and /var/log/tripal_cron.log log files.
 
 ## Data backup
 
@@ -131,7 +171,7 @@ services:
       - ./your/backed/up/dir/tripal_private:/var/www/private
       [...]
   db:
-    image: erasche/chado:latest
+    image: erasche/chado
     [...]
     volumes:
       - ./your/backed/up/dir/tripal_db:/var/lib/postgresql/data/

docker-compose.yml

@@ -16,7 +16,7 @@ services:
         MEMORY_LIMIT: 128M
         BASE_URL: "http://localhost:3000/tripal"
         BASE_URL_PROTO: "http://"
-        DB_NAME: 'tripal'
+        DB_NAME: 'postgres'
       ports:
         - "3000:80"
 

entrypoint.sh

@@ -69,10 +69,24 @@ fi
 
 
 ### Initial setup if database doesn't exist
+if [ "$(PGPASSWORD=$DB_PASS psql -U $DB_USER -h $DB_HOST -p $DB_PORT postgres -tAc "SELECT 1 FROM pg_database WHERE datname='$DB_NAME'" )" != '1' ]
+then
+    echo "Database $DB_NAME does not exist, creating it"
+    echo "CREATE DATABASE $DB_NAME;" | psql -U $DB_USER -h $DB_HOST -p $DB_PORT postgres;
+fi
+
+# Add possibly missing files/dirs if sites dir is empty (files needed by drush pm-list)
+if [ ! -e /var/www/html/sites/default ]; then
+    mkdir -p /var/www/html/sites/default/
+fi
+
+if [ ! -e /var/www/html/sites/default/settings.php ]; then
+    cp /etc/tripal/settings.php /var/www/html/sites/default/settings.php
+fi
 
 # Check if tables are there and that drush works
 DB_LOADED=$(PGPASSWORD=$DB_PASS psql -U "$DB_USER" -h "$DB_HOST" -p "$DB_PORT" -tAc "SELECT EXISTS (SELECT 1 FROM information_schema.tables WHERE table_name = 'organism');")
-DRUSH_OK=`drush pm-list > /dev/null 2>&1; echo "$?"`
+DRUSH_OK=`export ENABLE_MEMCACHE=0 && drush pm-list > /dev/null 2>&1; echo "$?"`
 if [[ $DRUSH_OK != "0" && $DB_LOADED != "t" ]]
 then
 	run_scripts setup
@@ -89,10 +103,10 @@ then
 elif [[ $DRUSH_OK != "0" && $DB_LOADED == "t" ]]
 then
 	echo "=> Error: 'drush pm-list' fails but the database is not empty. Something is wrong in the install. Exiting."
-    drush pm-list
+    export ENABLE_MEMCACHE=0 && drush pm-list
     exit $?
 else
-	echo "=> Skipped setup - database ${DB_NAME} already exists."
+	echo "=> Skipped setup - database ${DB_NAME} already ready."
 fi
 
 

etc/tripal/settings.php

@@ -21,7 +21,7 @@ $conf['mail_system'] = ['default-system' => 'TestingMailSystem'];
 /**
  * Default elasticsearch host
  */
-$conf['elasticsearch_hosts'] = array('elasticsearch');
+$conf['elasticsearch_host'] = 'elasticsearch';
 
 /**
  * Caching
@@ -31,6 +31,18 @@ if (getenv('ENABLE_DRUPAL_CACHE') == "1") {
     $conf['block_cache'] = TRUE;
 }
 
+if (getenv('ENABLE_MEMCACHE') == "1" && file_exists($_SERVER{'DOCUMENT_ROOT'} . '/sites/all/modules/memcache/memcache.inc')) {
+    $conf['cache_backends'][] = 'sites/all/modules/memcache/memcache.inc';
+    $conf['cache_default_class'] = 'MemCacheDrupal';
+    $conf['cache_class_cache_form'] = 'DrupalDatabaseCache';
+    $conf['page_cache_without_database'] = TRUE;
+    $conf['page_cache_invoke_hooks'] = FALSE;
+
+    // Use memcache for locking mechanisms
+    $conf['ultimate_cron_class_lock'] = 'UltimateCronLockMemcache';
+    $conf['lock_inc'] = 'sites/all/modules/memcache/memcache-lock.inc';
+}
+
 if (getenv('BASE_URL'))
     // Use BASE_URL if defined by user
     $base_url = getenv('BASE_URL');

scripts/pre-launch.d/00conf_php

@@ -11,3 +11,11 @@ then
 else
     echo "PHP OPcache disabled"
 fi
+
+if [[ $ENABLE_MEMCACHE == "1" ]]
+then
+    echo "Memcache enabled"
+    echo "extension=memcached.so" > $PHP_INI_DIR'/conf.d/memcached-status.ini'
+else
+    echo "Memcache disabled"
+fi

scripts/pre-launch.d/08memcache

+if [[ $ENABLE_MEMCACHE == "1" ]]
+then
+    service memcached start
+fi

scripts/pre-launch.d/10cron

 # Launch tripal jobs regularly
 chmod a+x /root/
 
-echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"/usr/local/bin/drush trp-run-jobs --username=${ADMIN_USER}\"') >> /var/log/tripal_jobs.log 2>&1" > tripal_cron
-echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elastic_queue_0\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
-echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elastic_queue_1\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
-echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elastic_queue_2\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
-echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elastic_queue_3\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
-echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elastic_queue_4\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
-echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elastic_queue_5\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
-echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elastic_queue_6\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
-echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elastic_queue_7\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
-echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elastic_queue_8\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
-echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elastic_queue_9\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
-crontab tripal_cron && rm tripal_cron
+if [[ $ENABLE_CRON_JOBS == "1" ]]
+then
+    echo "Tripal job launching scheduled with cron"
 
-service cron start
+    echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"/usr/local/bin/drush trp-run-jobs --username=${ADMIN_USER}\"') >> /var/log/tripal_jobs.log 2>&1" > tripal_cron
+    echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_0\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
+    echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_1\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
+    echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_2\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
+    echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_3\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
+    echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_4\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
+    echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_5\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
+    echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_6\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
+    echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_7\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
+    echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_8\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
+    echo "*/2 * * * * (bash -lc 'cd /var/www/html; su www-data -s /bin/bash -c \"export BASE_URL=http://localhost/ && /usr/local/bin/drush cron-run queue_elasticsearch_queue_9\"') >> /var/log/tripal_cron.log 2>&1" >> tripal_cron
+    crontab tripal_cron && rm tripal_cron
+
+    service cron start
+fi

scripts/pre-launch.d/20check_settings

@@ -10,6 +10,7 @@ if [ ! -e /var/www/html/sites/all ]; then
     mkdir -p /var/www/html/sites/all/themes/
 fi
 
+# This is probably already done in entrypoint.sh, but just in case
 if [ ! -e /var/www/html/sites/default/settings.php ]; then
     cp /etc/tripal/settings.php /var/www/html/sites/default/settings.php
 fi

scripts/pre-launch.d/40ext_libs

+# This script will ensure all required modules are installed and enabled
+
+cd /var/www/html/
+
+if [[ ! $(ls -A /var/www/html/sites/all/libraries/) ]]; then
+    # If no library is present in libraries dir, it (probably) means we are mounting an empty dir
+    # Make sure mandatory libraries are installed there
+
+    echo "Could not find required external libraries, reinstalling them in /var/www/html/sites/all/libraries/"
+
+    cd /var/www/html/sites/all/libraries/
+
+    mkdir elasticsearch-php
+
+    cd elasticsearch-php
+
+    composer require "elasticsearch/elasticsearch:~5.0"
+
+    cd /var/www/html/
+fi

scripts/pre-launch.d/50modules

+# This script will ensure all required modules are installed and enabled
+
+cd /var/www/html/
+
+if [[ ! $(ls -A /var/www/html/sites/all/modules/) ]]; then
+    # If no module is present in module dir, it (probably) means we are mounting an empty dir
+    # Make sure mandatory modules are installed there
+    # No real download from drupal.org will be done, tarballs are cached by drush when building the image
+
+    echo "Could not find required base modules, reinstalling them in /var/www/html/sites/all/modules/"
+
+    # Fetch the tripal code from github repo (drupal.org repo is often outdated)
+    cd /var/www/html/sites/all/modules/
+    repo_url=`echo $TRIPAL_BASE_CODE_GIT | sed 's/\(.\+\)\[@\w\+\]/\1/'`
+    rev=`echo $TRIPAL_BASE_CODE_GIT | sed 's/.\+\[@\(\w\+\)\]/\1/'`
+    git clone $repo_url tripal
+    cd tripal
+    if [ "$repo_url" != "$rev" ]; then
+        git reset --hard $rev
+    fi
+    cd /var/www/html/
+
+    # Fetch the other modules from drupal.org
+    drush pm-download ctools views libraries services ultimate_cron memcache
+
+    # Patch views module
+    cd /var/www/html/sites/all/modules/views
+    patch -p1 < ../tripal/tripal_views/views-sql-compliant-three-tier-naming-1971160-30.patch
+    cd /var/www/html/
+fi
+
+# Make sure all required modules are enabled
+drush pm-enable ctools views views_ui libraries services
+drush pm-enable rest_server ultimate_cron
+drush pm-enable tripal_core
+drush pm-enable tripal_views tripal_db tripal_cv tripal_organism tripal_analysis tripal_feature
+
+if [[ $ENABLE_MEMCACHE == "1" ]]
+then
+    # This always returns an error, just ignore it, it will work.
+    drush pm-enable memcache || true
+fi
+
+# Make sure permissions are ok
+drush role-add-perm 'anonymous user' 'access chado_analysis content'
+drush role-add-perm 'anonymous user' 'access chado_feature content'
+drush role-add-perm 'anonymous user' 'access chado_organism content'
+drush role-add-perm 'authenticated user' 'access chado_analysis content'
+drush role-add-perm 'authenticated user' 'access chado_feature content'
+drush role-add-perm 'authenticated user' 'access chado_organism content'
+
+
+# Install additional modules
+# We don't want to overwrite existing modules to avoid unexpected changes in module code
+
+# Temporary disable default settings to allow usage of --no option
+if [ -f /etc/drush/drushrc.php ]; then
+    mv /etc/drush/drushrc.php /etc/drush/drushrc.php_back
+fi
+
+if [ ! -z "$TRIPAL_DOWNLOAD_MODULES" ]; then
+    drush pm-download --no ${TRIPAL_DOWNLOAD_MODULES}
+fi
+
+if [ -f /etc/drush/drushrc.php_back ]; then
+    mv /etc/drush/drushrc.php_back /etc/drush/drushrc.php
+fi
+
+
+if [ ! -z "$TRIPAL_GIT_CLONE_MODULES" ]; then
+    cd /var/www/html/sites/all/modules/
+    for repo in $TRIPAL_GIT_CLONE_MODULES; do
+        repo_url=`echo $repo | sed 's/\(.\+\)\[@\w\+\]/\1/'`
+        rev=`echo $repo | sed 's/.\+\[@\(\w\+\)\]/\1/'`
+        module_name=`basename $repo_url .git`
+        if [ -d "$module_name" ]; then
+            echo "Skipping git clone of module $module_name from $repo_url, $module_name already exists in /var/www/html/sites/all/modules/$module_name"
+        else
+            git clone $repo_url
+            if [ "$repo_url" != "$rev" ]; then
+                cd "$module_name"
+                git reset --hard $rev
+                cd /var/www/html/sites/all/modules/
+            fi
+        fi
+    done
+    cd /var/www/html/
+fi
+
+drush pm-enable ${TRIPAL_ENABLE_MODULES}
+
+# Launch any job automatically created while installing modules
+drush trp-run-jobs --username=${ADMIN_USER}
+
+
+# Make sure module permissions are ok too (if modules are installed)
+drush role-add-perm 'anonymous user' 'access chado_analysis_go content' || true
+drush role-add-perm 'anonymous user' 'access chado_analysis_blast content' || true
+drush role-add-perm 'anonymous user' 'access chado_analysis_interpro content' || true
+drush role-add-perm 'authenticated user' 'access chado_analysis_go content' || true
+drush role-add-perm 'authenticated user' 'access chado_analysis_blast content' || true
+drush role-add-perm 'authenticated user' 'access chado_analysis_interpro content' || true
+
+
+# Install additional themes
+
+if [ ! -z "$THEME_GIT_CLONE" ]; then
+    cd /var/www/html/sites/all/themes/
+    for repo in $THEME_GIT_CLONE; do
+        theme_name=`basename $repo .git`
+        if [ -d "$theme_name" ]; then
+            echo "Skipping git clone of theme $theme_name from $repo, $theme_name already exists in /var/www/html/sites/all/themes/$theme_name"
+        else
+            git clone $repo
+        fi
+    done
+    cd /var/www/html/
+fi
+
+if [ ! -z "$THEME" ]; then
+    # Activate the theme
+    drush pm-enable "$THEME"
+    drush vset theme_default "$THEME"
+fi
+
+
+
+# Clear cache
+drush cc all

scripts/pre-launch.d/99file_perm

 prev_dir=$(pwd)
 
 cd /var/www
-chown -R www-data.www-data .
-find . -type d -exec chmod ug=rx,o= '{}' \;
-find . -type f -exec chmod ug=r,o= '{}' \;
+chown -Rf www-data.www-data . || echo
+find . -type d -exec chmod -f ug=rx,o= '{}' \; || echo
+find . -type f -exec chmod -f ug=r,o= '{}' \; || echo
 
+mkdir -p private
 chmod ug=rwx,o= private
 find private -type d -exec chmod ug=rwx,o= '{}' \;
 find private -type f -exec chmod ug=rw,o= '{}' \;

scripts/pre-launch.d/README.txt

 This folder contains scripts that will be executed before the launch of a Drupal-instance.
-See /README.md for details.

scripts/setup.d/20check_settings

@@ -14,5 +14,5 @@ if [ ! -e /var/www/html/sites/default/settings.php ]; then
     cp /etc/tripal/settings.php /var/www/html/sites/default/settings.php
 fi
 
-chown -R www-data.www-data /var/www/html/sites
-chown -R www-data.www-data /var/www/private
+chown -Rf www-data.www-data /var/www/html/sites || echo
+chown -Rf www-data.www-data /var/www/private || echo

scripts/setup.d/40site-install → scripts/setup.d/40site_install

 /usr/bin/env PHP_OPTIONS="-d sendmail_path=$(which true)" drush site-install --site-name=default --account-name="${ADMIN_USER}" --account-pass="${ADMIN_PASSWORD}"
+
+patch -p1 < /drupal.pgsql-bytea.27.patch

scripts/setup.d/50chado_install

+# Install the chado db
+
+export PGPASSWORD=$DB_PASS
+gunzip -f /chado-master-tripal.sql.gz
+# Set the search path to something useful
+echo "alter database $DB_NAME set search_path = '$user',public,chado;" | psql -U $DB_USER -h $DB_HOST -p $DB_PORT $DB_NAME;
+psql -U $DB_USER -h $DB_HOST -p $DB_PORT $DB_NAME -f /chado-master-tripal.sql
+echo "CREATE INDEX bingroup_boxrange ON featuregroup USING gist (chado.boxrange(fmin, fmax)) WHERE (is_root = 1);" | psql -U $DB_USER -h $DB_HOST -p $DB_PORT $DB_NAME;
+psql -U $DB_USER -h $DB_HOST -p $DB_PORT $DB_NAME -f /search.sql

scripts/setup.d/50tripal_chado_install

-export PGPASSWORD=$DB_PASS
-gunzip /chado-master-tripal.sql.gz
-# Set the search path to something useful
-echo "alter database $DB_NAME set search_path = '$user',public,chado;" | psql -U $DB_USER -h $DB_HOST -p $DB_PORT $DB_NAME;
-psql -U $DB_USER -h $DB_HOST -p $DB_PORT $DB_NAME -f /chado-master-tripal.sql
-echo "CREATE INDEX bingroup_boxrange ON featuregroup USING gist (chado.boxrange(fmin, fmax)) WHERE (is_root = 1);" | psql -U $DB_USER -h $DB_HOST -p $DB_PORT $DB_NAME;
-psql -U $DB_USER -h $DB_HOST -p $DB_PORT $DB_NAME -f /search.sql
-
-drush pm-download ctools views tripal-7.x-2.x-dev
-drush pm-enable ctools views views_ui libraries services
-drush pm-enable rest_server ultimate_cron
-
-wget --no-check-certificate https://drupal.org/files/drupal.pgsql-bytea.27.patch && patch -p1 < drupal.pgsql-bytea.27.patch
-
-cd /var/www/html/sites/all/modules/views
-patch -p1 < ../tripal/tripal_views/views-sql-compliant-three-tier-naming-1971160-30.patch
-
-cd /var/www/html/
-
-drush pm-enable tripal_core
-
-if [ ! -z "$TRIPAL_DOWNLOAD_MODULES" ]; then
-    drush pm-download ${TRIPAL_DOWNLOAD_MODULES}
-fi
-if [ ! -z "$TRIPAL_GIT_CLONE_MODULES" ]; then
-    cd /var/www/html/sites/all/modules/
-    for repo in $TRIPAL_GIT_CLONE_MODULES; do
-        git clone $repo
-    done
-    cd /var/www/html/
-fi
-
-if [ ! -z "$THEME_GIT_CLONE" ]; then
-    cd /var/www/html/sites/all/themes/
-    for repo in $THEME_GIT_CLONE; do
-        git clone $repo
-    done
-    cd /var/www/html/
-fi
-
-if [ ! -z "$THEME" ]; then
-    # Activate the theme
-    drush pm-enable "$THEME"
-    drush vset theme_default "$THEME"
-fi
-
-drush pm-enable tripal_views tripal_db tripal_cv tripal_organism tripal_analysis tripal_feature ${TRIPAL_ENABLE_MODULES}
-
-# Ensure permissions are available
-drush role-add-perm 'anonymous user' 'access chado_analysis content'
-drush role-add-perm 'anonymous user' 'access chado_feature content'
-drush role-add-perm 'anonymous user' 'access chado_organism content'
-drush role-add-perm 'authenticated user' 'access chado_analysis content'
-drush role-add-perm 'authenticated user' 'access chado_feature content'
-drush role-add-perm 'authenticated user' 'access chado_organism content'
-
-# Launch jobs automatically created
-drush trp-run-jobs --username=${ADMIN_USER}

scripts/setup.d/README.txt

 This folder contains scripts that will be executed as installation-process of a
-Drupal-instance. See /README.md for details.
+Drupal-instance.