Write new Dockerfile, using apt and prebuilt binaries where possible

Author: kevinlul

.dockerignore

@@ -1 +1,2 @@
 *
+!config-template

Dockerfile

@@ -1,36 +1,40 @@
 FROM ubuntu/apache2:2.4-20.04_beta
 
-RUN ln -sf /dev/stdout /var/log/apache2/access.log && ln -sf /dev/stderr /var/log/apache2/error.log && a2enmod cgi
-RUN apt update -y && apt install -y mongodb ca-certificates curl python python3-pip && rm -rf /var/lib/apt/lists/* && curl https://bootstrap.pypa.io/pip/2.7/get-pip.py | python 
-RUN pip install --no-cache-dir numpy==1.11.2 pymongo==3.8.0 requests==2.22.0 && pip3 install --no-cache-dir numpy==1.17.2 pymongo==3.8.0 requests==2.20.0 Jinja2==2.10.1 GitPython==3.0.5
+# Match Docker expectations for logging like the Docker Library nginx image
+RUN ln -sf /dev/stdout /var/log/apache2/access.log && \
+    ln -sf /dev/stderr /var/log/apache2/error.log && \
+# Enable Common Gateway Interface scripts that comprise much of FORCAST's backend
+    a2enmod cgi
+RUN apt update -y && \
+    apt install -y \
+# MongoDB 3.6 for storing guides and primers
+        mongodb \
+# General downloads here, unzip JBrowse
+        ca-certificates curl unzip \
+# Convenient downloads for Dicey from GEAR Genomics Tracy
+        wget rename \
+# FORCAST uses both Python 2 and 3 for some reason
+        python python3-pip \
+# Bioinformatics tools used when installing new genomes
+        bwa bedtools samtools ncbi-blast+ && \
+# FORCAST primer design feature after setup
+        primer3 && \
+# Remove lists pulled by apt update for consistent images
+    rm -rf /var/lib/apt/lists/* && \
+# python-pip is no longer included in the distribution as Python 2 is out of support
+    curl https://bootstrap.pypa.io/pip/2.7/get-pip.py | python
+RUN mkdir -p /opt/dicey/bin && \
+    mkdir -p /opt/dicey/dicey_tempfiles && \
+    curl -Lo /opt/dicey/bin/dicey https://github.com/gear-genomics/dicey/releases/download/v0.1.8/dicey_v0.1.8_linux_x86_64bit && \
+    chmod +x /opt/dicey/bin/dicey
+ARG JBROWSE_VERSION=1.12.3
+RUN curl -LO https://jbrowse.org/releases/JBrowse-${JBROWSE_VERSION}/JBrowse-${JBROWSE_VERSION}.zip && \
+    unzip JBrowse-${JBROWSE_VERSION}.zip && \
+    mv JBrowse-${JBROWSE_VERSION} /var/www/html/jbrowse && \
+    rm JBrowse-${JBROWSE_VERSION}.zip && \
+    cd /var/www/html/jbrowse && ./setup.sh
+RUN pip install --no-cache-dir numpy==1.11.2 pymongo==3.8.0 requests==2.22.0 && \
+    pip3 install --no-cache-dir numpy==1.17.2 pymongo==3.8.0 requests==2.20.0 Jinja2==2.10.1 GitPython==3.0.5
+COPY config-template /var/www/html/config
 
 CMD service mongodb start && exec apache2-foreground
-# Install JBrowse
-# Install GuideFinder dependencies?
-# Install Primer3, NCBI Blast, Dicey
-
-
-
-#FROM ubuntu:16.04
-#LABEL maintainer="[email protected]"
-#ENV DEBIAN_FRONTEND noninteractive
-
-# INSTALL BASE REQUIREMENTS
-#RUN apt-get update && \
-#    apt-get install -y git sudo apache2 && \
-#    cd /var/www/html && \
-#    rm index.html
-
-# CHANGE DOCUMENT ROOT AND SERVERNAME
-#WORKDIR /etc/apache2
-#RUN sed -i -e "/DocumentRoot/a \ \t\<Directory \'\/var\/www\/html\'\>\n\t\tOptions +ExecCGI\n\t\tAddHandler cgi-script .py\n\t\tAllow from all\n\t</Directory\>" sites-available/000-default.conf
-#RUN sed -i '1 i\ServerName FORCAST' apache2.conf
-
-# GET HOST CODE
-#COPY . /var/www/html/
-#WORKDIR /var/www/html/
-
-# INSTALL DEPENDENCIES
-#RUN cd src/installation && \
-#    ./install.sh /var/www/html && \
-#    ./setPermissions.sh

docker-compose.yaml

@@ -1,47 +1,27 @@
 version: "3.9"
 services:
-  # mongo:
-  #   image: mongo:3.6
-  #   ports:
-  #     - 127.0.0.1:27017:27017
   forcast:
     build: .
     image: ghcr.io/ccmbioinfo/forcast
     ports:
       - 80:80
     volumes:
       - ./sites-enabled:/etc/apache2/sites-enabled
-      - ./:/var/www/html
+      - ./bin:/var/www/html/bin
+      - ./docs:/var/www/html/docs
+      - ./src:/var/www/html/src
+      - ./jbrowse/plugins/ColorByCDS:/var/www/html/jbrowse/plugins/ColorByCDS
+      - ./jbrowse/plugins/ExportSequence:/var/www/html/jbrowse/plugins/ExportSequence
+      - ./crispr-icon.png:/var/www/html/crispr-icon.png
+      - ./index.html:/var/www/html/index.html
       - mongodb:/var/lib/mongodb
 volumes:
   mongodb:
 
-
-
-# Install genome and enable dicey
-
-
-
-#version: '2'
-
-#services:
-#    webserver:
-#        image: helrick/forcast
-#        expose:
-#            - ${APACHE2_PORT}
-#        ports:
-#            - ${APACHE2_PORT}:${APACHE2_PORT}
-#        volumes:
-#            - ./mongodb:/data/db
-#            - ./src:/var/www/html/src
-#            - ./jbrowse:/var/www/html/jbrowse
-#        command: >
-#            bash -c "sudo mongod --fork --logpath /var/log/mongodb.log
-#            && cd /var/www/html/jbrowse
-#            && ./setup.sh
-#            && python3 /var/www/html/src/setup/setup.py -r /var/www/html -g ${ORGANISM} -v ${ASSEMBLY} -fa2bit /var/www/html/bin/faToTwoBit -b /var/www/html/bin/ncbi-blast-2.7.1+/bin
-#            && /var/www/html/src/setup/enable_dicey.sh ${ORGANISM} ${ASSEMBLY}
-#            && cd /var/www/html/src/installation
-#            && sudo ./setPermissions.sh
-#            && sudo service apache2 start
-#            && tail -f /dev/null"
+# After startup, exec into the container and run
+# cd /var/www/html/src/setup
+# python3 setup.py -r /var/www/html -g Saccharomyces_cerevisiae -v R64-1-1 -fa2bit /var/www/html/bin/faToTwoBit -b /usr/bin
+# mkdir -p /opt/dicey/indexes/R64-1-1
+# cd /opt/dicey/indexes/R64-1-1
+# wget -r -np -nH --cut-dirs 2 -A "Saccharomyces_cerevisiae.*" https://gear.embl.de/data/tracy/
+# rename "s/^.*.fa\./R64-1-1.fa./" *