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Docker db decouple #89

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merged 3 commits into from
Oct 9, 2019
Merged

Docker db decouple #89

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3d36c4f
make requirements more lenient, text formatting
matthdsm Aug 19, 2019
f6cdf88
simplify docker image, decouple db, db settings settable with ENV var…
matthdsm Aug 19, 2019
cf06e56
fix double multiqc install
matthdsm Aug 19, 2019
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86 changes: 14 additions & 72 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,78 +1,20 @@
FROM debian:latest
FROM tiangolo/meinheld-gunicorn-flask:python3.7

LABEL authors="[email protected],[email protected]" \
description="Docker image running MegaQC"

# Install container-wide requrements
RUN apt-get update && apt-get install git -y && \
apt-get install python2.7 -y && \
apt-get install python2.7-dev -y && \
apt-get install libyaml-dev -y && \
apt-get install libffi-dev -y && \
apt-get install libpng-dev -y && \
apt-get install libfreetype6-dev -y && \
apt-get install curl -y && \
apt-get install gcc -y && \
apt-get install g++ -y && \
apt-get install apache2 -y

# Enable apache mod_proxy
RUN a2enmod proxy
RUN a2enmod proxy_http

# Overwrite apache config
RUN echo "<VirtualHost *:80> \n\
ServerName megaqc \n\
ProxyPass / http://127.0.0.1:8000/ \n\
ProxyPassReverse / http://127.0.0.1:8000/ \n\
</VirtualHost>" > /etc/apache2/sites-enabled/000-default.conf

# Fix matplotlib being dumb
RUN ln -s /usr/include/freetype2/ft2build.h /usr/include/

# Link python
RUN ln -s /usr/bin/python2.7 /usr/bin/python

# Install pip
RUN curl -fsSL https://bootstrap.pypa.io/get-pip.py -o /opt/get-pip.py && \
python /opt/get-pip.py && \
rm /opt/get-pip.py

# Install PostgreSQL and psycopg2
RUN apt-get install postgresql-9.6 postgresql-server-dev-9.6 -y

# Set data directory
ENV PGDATA /usr/local/lib/postgresql

# Tell MegaQC to use postgres / psycopg2
ENV MEGAQC_PRODUCTION 1

# create the data directory
RUN mkdir $PGDATA
RUN chown postgres $PGDATA
# Start postgres
# Create the basic requirements
RUN su postgres -c "/usr/lib/postgresql/9.6/bin/initdb" && \
su postgres -c "/usr/lib/postgresql/9.6/bin/pg_ctl -D $PGDATA -w start" && \
su postgres -c "/usr/lib/postgresql/9.6/bin/createuser megaqc_user" && \
su postgres -c "/usr/lib/postgresql/9.6/bin/createdb megaqc -O megaqc_user" && \
su postgres -c "/usr/lib/postgresql/9.6/bin/pg_ctl -D $PGDATA -w stop"

# Install MegaQC
COPY . MegaQC
WORKDIR MegaQC
RUN python setup.py install

# Set up the Postgres SQL server
RUN su postgres -c "/usr/lib/postgresql/9.6/bin/pg_ctl -D $PGDATA -w start" && \
megaqc initdb && \
su postgres -c "/usr/lib/postgresql/9.6/bin/pg_ctl -D $PGDATA -w stop"

# Use volumes to persist logs and data
VOLUME ["/var/log/postgresql", "/usr/local/lib/postgresql"]

# Run the MegaQC server
EXPOSE 80
CMD su postgres -c "/usr/lib/postgresql/9.6/bin/pg_ctl -D $PGDATA -w start" && \
service apache2 start && \
gunicorn megaqc.wsgi:app --timeout 300
ENV MEGAQC_PRODUCTION=1 \
MEGAQC_SECRET="SuperSecretValueYouShouldReallyChange" \
MEGAQC_CONFIG="" \
APP_MODULE=megaqc.wsgi:app\
DB_HOST="127.0.0.1" \
DB_PORT="5432" \
DB_NAME="megaqc" \
DB_USER="megaqc" \
DB_PASS="megaqcpswd"

COPY . /app

RUN python /app/setup.py install
9 changes: 6 additions & 3 deletions megaqc/settings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,15 +67,18 @@ def update_db_uri(self):
self.SQLALCHEMY_DATABASE
)


class ProdConfig(Config):
"""Production configuration."""

ENV = 'prod'
DEBUG = False
SQLALCHEMY_DBMS = 'postgresql'
SQLALCHEMY_USER = 'megaqc_user'
SQLALCHEMY_HOST = 'localhost:5432'
SQLALCHEMY_DATABASE = 'megaqc'
SQLALCHEMY_HOST = "{}:{}".format(os.environ.get(
'DB_HOST', 'localhost'), os.environ.get('DB_PORT', '5432'))
SQLALCHEMY_USER = os.environ.get('DB_USER', 'megaqc')
SQLALCHEMY_PASS = os.environ.get('DB_PASS', 'megaqcpswd')
SQLALCHEMY_DATABASE = os.environ.get('DB_NAME', 'megaqc')
DEBUG_TB_ENABLED = False # Disable Debug toolbar

def __init__(self):
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71 changes: 37 additions & 34 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,43 +21,45 @@
"Flask-Caching>=1.0.0",
"Flask-DebugToolbar>=0.10.1",
"Flask-Login>=0.4.0",
"Flask-SQLAlchemy==2.2",
"Flask-WTF==0.14.2",
"Flask-SQLAlchemy>=2.2",
"Flask-WTF>=0.14.2",
"Flask==1.0.2",
"future==0.16.0",
"itsdangerous>=0.24",
"Jinja2>=2.9.5",
"markdown>=2.6.11",
"numpy==1.14.3",
"multiqc>=1.3",
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Same here

"numpy>=1.14.3",
"passlib==1.7.1",
"plotly==2.0.15",
"pyyaml==3.12",
"pyyaml>=3.12",
"SQLAlchemy>=1.1.5",
"Werkzeug==0.14.1",
"Werkzeug>=0.14.1",
"WTForms>=2.1",

# Testing
"pytest==3.0.6",
"WebTest==2.0.26",
"factory-boy==2.8.1",
"livereload==2.5.1",
"pytest>=3.0.6",
"WebTest>=2.0.26",
"factory-boy>=2.8.1",
"livereload>=2.5.1",

# Lint and code style
#"flake8==3.3.0",
#flake8-blind-except==0.1.1",
#"flake8-debugger==1.4.0",
#"flake8-docstrings==1.0.3",
#"flake8-isort==2.1.3",
#"flake8-quotes==0.9.0",
#"isort==4.2.5",
#"pep8-naming==0.4.1",
# "flake8==3.3.0",
# flake8-blind-except==0.1.1",
# "flake8-debugger==1.4.0",
# "flake8-docstrings==1.0.3",
# "flake8-isort==2.1.3",
# "flake8-quotes==0.9.0",
# "isort==4.2.5",
# "pep8-naming==0.4.1",
]

prod_reqs = dev_reqs + [
"psycopg2-binary>=2.6.2",
"gunicorn>=19.7.1",
]
install_requires = prod_reqs if os.environ.get('MEGAQC_PRODUCTION') else dev_reqs
install_requires = prod_reqs if os.environ.get(
'MEGAQC_PRODUCTION') else dev_reqs


print("""-----------------------------------
Expand All @@ -67,22 +69,23 @@
""".format(version))

setup(
name = 'megaqc',
version = version,
author = 'Phil Ewels',
author_email = '[email protected]',
description = "Collect and visualise data across multiple MultiQC runs",
long_description = __doc__,
keywords = ['bioinformatics', 'biology', 'sequencing', 'NGS', 'next generation sequencing', 'quality control'],
url = 'https://megaqc.info/',
download_url = 'https://github.com/ewels/MegaQC/releases',
license = 'GPLv3',
packages = ['megaqc'],
include_package_data = True,
zip_safe = False,
scripts = ['scripts/megaqc'],
install_requires = install_requires,
classifiers = [
name='megaqc',
version=version,
author='Phil Ewels',
author_email='[email protected]',
description="Collect and visualise data across multiple MultiQC runs",
long_description=__doc__,
keywords=['bioinformatics', 'biology', 'sequencing', 'NGS',
'next generation sequencing', 'quality control'],
url='https://megaqc.info/',
download_url='https://github.com/ewels/MegaQC/releases',
license='GPLv3',
packages=['megaqc'],
include_package_data=True,
zip_safe=False,
scripts=['scripts/megaqc'],
install_requires=install_requires,
classifiers=[
'Development Status :: 4 - Beta',
'Environment :: Console',
'Environment :: Web Environment',
Expand Down