Ongoing work to restore reproducible builds

Missing JBrowse, Primer3, BLAST, Dicey installs

Author: kevinlul

.dockerignore

@@ -0,0 +1 @@
+*

.editorconfig

@@ -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

Dockerfile

@@ -1,23 +1,36 @@
-FROM ubuntu:16.04
-LABEL maintainer="[email protected]"
-ENV DEBIAN_FRONTEND noninteractive
+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
+
+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
+#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
+#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/
+#COPY . /var/www/html/
+#WORKDIR /var/www/html/
 
 # INSTALL DEPENDENCIES
-RUN cd src/installation && \
-    ./install.sh /var/www/html && \
-    ./setPermissions.sh
+#RUN cd src/installation && \
+#    ./install.sh /var/www/html && \
+#    ./setPermissions.sh

docker-compose.yaml

@@ -1,23 +1,47 @@
-version: '2'
-
+version: "3.9"
 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"
+  # 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
+      - 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"

sites-enabled/000-default.conf

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+<VirtualHost *:80>
+	# The ServerName directive sets the request scheme, hostname and port that
+	# the server uses to identify itself. This is used when creating
+	# redirection URLs. In the context of virtual hosts, the ServerName
+	# specifies what hostname must appear in the request's Host: header to
+	# match this virtual host. For the default virtual host (this file) this
+	# value is not decisive as it is used as a last resort host regardless.
+	# However, you must set it for any further virtual host explicitly.
+	#ServerName www.example.com
+
+	ServerAdmin webmaster@localhost
+	DocumentRoot /var/www/html
+
+	# Available loglevels: trace8, ..., trace1, debug, info, notice, warn,
+	# error, crit, alert, emerg.
+	# It is also possible to configure the loglevel for particular
+	# modules, e.g.
+	#LogLevel info ssl:warn
+
+	ErrorLog ${APACHE_LOG_DIR}/error.log
+	CustomLog ${APACHE_LOG_DIR}/access.log combined
+
+	# For most configuration files from conf-available/, which are
+	# enabled or disabled at a global level, it is possible to
+	# include a line for only one particular virtual host. For example the
+	# following line enables the CGI configuration for this host only
+	# after it has been globally disabled with "a2disconf".
+	#Include conf-available/serve-cgi-bin.conf
+
+	# FORCAST modification from base configuration
+	<Directory "/var/www/html">
+		Options +ExecCGI
+		AddHandler cgi-script .py
+		Require all granted
+	</Directory>
+	# End modification
+</VirtualHost>
+
+# vim: syntax=apache ts=4 sw=4 sts=4 sr noet