Refactor Docker image to use Python 3 via micromamba

This commit also includes some cleanup and refactoring of the Dockerfiles. This
also merges the previously separate Dockerfiles.

Currently this assumes that the Python 3 version of the CRISPResso2 source code
is found in the root directory of the project under the name `CRISPResso2`.

Dockerfile

@@ -4,50 +4,100 @@
 
 # Set the base image to anaconda python 2.7
 #FROM kclem/c2wbase:1.1
-FROM c2wbase:1.2
+FROM mambaorg/micromamba:0.13.1
 
 # File Author / Maintainer
 MAINTAINER Kendell Clement
 
 ENV SHELL bash
 
-#install CRISPResso
+
+# Install dependencies
+ENV DEBIAN_FRONTEND=noninteractive
+RUN echo "deb http://http.us.debian.org/debian buster main contrib" >> /etc/apt/sources.list && \
+    echo "deb http://security.debian.org buster/updates main contrib" >> /etc/apt/sources.list && \
+    apt-get update && \
+    apt-get install -y --no-install-recommends \
+    apache2 \
+    apache2-dev \
+    build-essential \
+    cron \
+    gcc \
+    libapache2-mod-wsgi \
+    rabbitmq-server \
+    ssl-cert \
+    ttf-mscorefonts-installer \
+    tmpreaper \
+    unzip \
+    wget \
+    zip && \
+    apt-get clean && \
+    apt-get autoremove -y && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install Micromamba
+RUN micromamba install -y -n base \
+    bowtie2 \
+    celery=4.4.6 \
+    cython \
+    email_validator \
+    flask \
+    flask-admin \
+    flask-mail \
+    flask-wtf \
+    flask-sqlalchemy \
+    flask-login \
+    flash \
+    numpy \
+    python=3.8 \
+    pip \
+    samtools \
+    sqlalchemy=1.3.23 \
+    trimmomatic \
+    werkzeug \
+    vine \
+    -c bioconda \
+    -c conda-forge && \
+    micromamba clean --all --yes && \
+    pip install mod_wsgi && \
+    mod_wsgi-express module-config > /etc/apache2/mods-available/wsgi.load
+
+# Install CRISPResso
 ARG crispresso_version='2.1.0'
 WORKDIR /tmp/CRISPResso2
-RUN wget https://github.com/pinellolab/CRISPResso2/archive/v${crispresso_version}.zip \
-  && unzip v${crispresso_version}.zip \
-  && cd /tmp/CRISPResso2/CRISPResso2-${crispresso_version} \
-  && python setup.py install \
-  && CRISPResso -h \
-  && rm -rf /tmp/CRISPResso2
+# RUN wget https://github.com/pinellolab/CRISPResso2/archive/v${crispresso_version}.zip \
+  # && unzip v${crispresso_version}.zip \
+COPY ./CRISPResso2 /tmp/CRISPResso2
+RUN cd /tmp/CRISPResso2/ && \
+    python setup.py install && \
+    CRISPResso -h && \
+    rm -rf /tmp/CRISPResso2
 
 #install flower
-#RUN conda install flower \
-#    && conda clean -ay
+#RUN micromamba install flower \
+#    && micromamba clean -ay
 
 ENV C_FORCE_ROOT "true"
 
 #install CRISPRessoWEB
 WORKDIR /var/www/webapps/CRISPRessoWEB
-RUN mkdir -p /var/www/CRISPResso_TMP/UPLOADS \
-  && mkdir -p /var/www/CRISPResso_TMP/REPORTS \
-  && mkdir -p /var/www/CRISPResso_TMP/DATA \
-  && mkdir -p /var/www/CRISPResso_TMP/SERVER \
-  && chmod -R 777 /var/www/CRISPResso_TMP
+RUN mkdir -p /var/www/CRISPResso_TMP/UPLOADS && \
+    mkdir -p /var/www/CRISPResso_TMP/REPORTS && \
+    mkdir -p /var/www/CRISPResso_TMP/DATA && \
+    mkdir -p /var/www/CRISPResso_TMP/SERVER && \
+    chmod -R 777 /var/www/CRISPResso_TMP
 COPY . /var/www/webapps/CRISPRessoWEB
 #RUN crontab add_to_crontab
-RUN cp conf_files/apache/httpd-vhosts.conf /etc/apache2/sites-available/crispresso.conf \
-  && cp conf_files/celery_daemon/celeryd /etc/init.d/ && chmod +x /etc/init.d/celeryd \
-  && chmod -R 755 /var/www/webapps/CRISPRessoWEB
-RUN a2ensite crispresso \
- && a2dissite 000-default
+RUN cp conf_files/apache/httpd-vhosts.conf /etc/apache2/sites-available/crispresso.conf && \
+    cp conf_files/celery_daemon/celeryd /etc/init.d/ && chmod +x /etc/init.d/celeryd && \
+    chmod -R 755 /var/www/webapps/CRISPRessoWEB
+RUN a2ensite crispresso && \
+    a2dissite 000-default
 
 #recreate demo files
 # WORKDIR /var/www/webapps/CRISPRessoWEB/CRISPRessoWEB/static/demo
 # RUN run.sh
 
-
-
 EXPOSE 80
 
 #flower port (activate flower in start_server_docker.sh)