Ich habe diese Web Anwendung https://github.com/nthomasCUBE/RNASeqExpressionBrowser gefunden und ich habe diese installation Anleitung https://www.youtube.com/watch?v=rTFIUnZDca8 befolgt und versucht diesen service mithilfe von docker-compose zum laufen zu bringen, aber leider funktioniert es nicht.
docker-compose.yml:
Code: Alles auswählen
version: '3'
services:
expressionbrowser:
build: .
restart: always
ports:
- "80:80"
depends_on:
- expressionbrowserdb
volumes:
- ./data/:/db
expressionbrowserdb:
image: mariadb
restart: always
environment:
- MYSQL_ROOT_PASSWORD=admin
- MYSQL_DATABASE=expressionbrowser
- MYSQL_USER=browseradmin
- MYSQL_PASSWORD=password
ports:
- "3306:3306"
volumes:
- ./mysql/:/docker-entrypoint-initdb.d
phpmyadmin:
image: phpmyadmin/phpmyadmin
restart: always
depends_on:
- expressionbrowserdb
ports:
- 8183:80
environment:
PMA_USER: root
PMA_PASSWORD: admin
PMA_ARBITRARY: 1
mysql/rna.sql
Code: Alles auswählen
CREATE DATABASE IF NOT EXISTS expressionbrowser;
CREATE USER 'browseradmin'@'localhost';
SET PASSWORD FOR 'browseradmin'@'localhost' = PASSWORD('password');
CREATE SCHEMA expressionbrowser;
GRANT ALL PRIVILEGES on expressionbrowser.* TO 'browseradmin'@'localhost';
Dockerfile:
Code: Alles auswählen
FROM debian:stretch-backports
RUN apt-get update && apt-get install -y --no-install-recommends \
build-essential \
apache2 \
python-dev \
python-setuptools \
python-numpy \
python-mysqldb \
python-pip \
python-wheel \
git wget unzip \
ncbi-blast+ && \
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
#Based on: https://github.com/eriston/Apache-with-python-cgi-Docker
#load apache cgi module
RUN a2enmod cgi
RUN service apache2 restart
#enable cgi in the website root
#second block to allow .htaccess
RUN echo " \n \
<Directory /var/www/html> \n \
Options +ExecCGI \n \
AddHandler cgi-script .py \n \
DirectoryIndex index.py \n \
</Directory> \n \
" >> /etc/apache2/apache2.conf
RUN chmod -R u+rwx,g+x,o+x /var/www/html
RUN pip install fisher goatools
RUN git clone https://github.com/nthomasCUBE/RNASeqExpressionBrowser.git
RUN example/example.zip
RUN cd RNASeqExpressionBrowser && \
sed -i.bak "s|mysql_host::server|mysql_host::expressionbrowserdb|" installation_example.conf && \
sed -i.bak "s|mysql_db::db|mysql_db::expressionbrowser|" installation_example.conf && \
sed -i.bak "s|mysql_user::user|mysql_user::browseradmin|" installation_example.conf && \
sed -i.bak 's|raw_input(">Please specify the absolute path to the directory where CSS file should be stored (within the /var/www/html directory, directory must exist) e.g. \[/var/www/html\]\\n") or my_input;|"/usr/lib/cgi-bin"|' installation.py && \
sed -i.bak 's|raw_input(">Please specify the absolute path to the directory of the web server location, somewhere under e.g. \[/var/www/cgi-bin OR /usr/lib/cgi-bin\]\\n")|"/var/www/html"|' installation.py && \
sed -i.bak 's|raw_input(">Please provide the path to the directory where R-output can be stored and accessed by apache-user e.g. \[/nfs/plantsp/webblast/data/\]\n")|"/data/webblast"|' installation.py #&& \
#python installation.py installation_example.conf
EXPOSE 80
CMD /usr/sbin/apache2ctl -D FOREGROUND
Vielen Dank im Voraus