ccmbioinfo
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diff --git a/‎.editorconfig
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diff --git a/‎.gitignore
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diff --git a/‎Dockerfile
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@@ -0,0 +1,2 @@
+*
+!config-template
@@ -0,0 +1,8 @@
+root = true
+
+[*]
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+max_line_length = 120
@@ -1,9 +1,7 @@
 # program/data folders
 .env
-bin/dicey
-bin/ncbi-blast-2.7.1+
-bin/primer3
-jbrowse/data.*
+bin/*
+jbrowse/data*
 jbrowse/Makefile
 jbrowse/setup.log
 jbrowse/jbrowse.conf
 
@@ -1,23 +1,52 @@
-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
+FROM ubuntu/apache2:2.4-20.04_beta
+# 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 && \
+# Enable mod_rewrite for the / homepage redirect
+    a2enmod rewrite && \
+# Disable directory listings. This is a core module, which requires --force
+    a2dismod --force autoindex
+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
+# In-silico PCR tool for primer design
+RUN curl -Lo /usr/local/bin/dicey https://github.com/gear-genomics/dicey/releases/download/v0.1.8/dicey_v0.1.8_linux_x86_64bit && \
+    chmod +x /usr/local/bin/dicey
+# UCSC Genome Browser kent binaries
+RUN curl -Lo /usr/local/bin/faToTwoBit https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit \
+         -Lo /usr/local/bin/twoBitToFa https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa && \
+    chmod +x /usr/local/bin/faToTwoBit /usr/local/bin/twoBitToFa
+RUN curl -LO https://github.com/GMOD/jbrowse/releases/download/1.12.5-release/JBrowse-1.12.5.zip && \
+    unzip JBrowse-1.12.5.zip && \
+    mv JBrowse-1.12.5 /var/www/html/jbrowse && \
+    rm JBrowse-1.12.5.zip && \
+    cd /var/www/html/jbrowse && ./setup.sh && \
+# Default FORCAST configuration for JBrowse. jbrowse/data/datasets.conf is bind-mounted for editing.
+    echo -e "classicMenu = true\ninclude += data/datasets.conf\n\n[aboutThisBrowser]\ntitle = FORCAST" >> /var/www/html/jbrowse/jbrowse.conf && \
+# Add favicon
+    sed -i '6i\    <link rel="icon" href="../docs/img/crispr-icon.png" sizes="100x100">' /var/www/html/jbrowse/index.html
+# Dependencies for FORCAST CGI scripts
+RUN pip install --no-cache-dir pymongo==3.12.3 requests==2.27.1 && \
+    pip3 install --no-cache-dir pymongo==3.12.3 requests==2.27.1 Jinja2==3.1.2
+COPY config-template /var/www/html/config
+WORKDIR /var/www/html
+# Replace the /usr/sbin/apachectl script that is called with the Apache master process that respects signals
+ENV APACHE_HTTPD exec /usr/sbin/apache2
+CMD service mongodb start && exec apache2-foreground