From fe31009bca753326b747e41b725f5eaa4e4ad5ab Mon Sep 17 00:00:00 2001 From: Alexandros Sigaras Date: Wed, 14 Mar 2018 17:09:18 -0400 Subject: [PATCH 1/5] Added git and docker ignore files --- .dockerignore | 2 ++ .gitignore | 0 Dockerfile | 10 +++++----- 3 files changed, 7 insertions(+), 5 deletions(-) create mode 100644 .dockerignore create mode 100644 .gitignore diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..934fce1 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,2 @@ +# Files to exclude during docker build +azuredeploy.json.template \ No newline at end of file diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..e69de29 diff --git a/Dockerfile b/Dockerfile index 4177ef1..531fd78 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,9 +4,9 @@ FROM python:2.7.14 # Setup Prerequisites # #=====================# RUN apt-get update && apt-get install -y \ - apache2 \ - git \ - vim \ + apache2 \ + git \ + vim \ && a2enmod cgi \ && service apache2 restart \ && rm -rf /var/lib/apt/lists/* @@ -14,8 +14,8 @@ RUN apt-get update && apt-get install -y \ # Docker Image Configuration # #===============================# LABEL Description='Beacon' \ - Vendor='Englander Institute for Precision Medicine' \ - maintainer='als2076@med.cornell.edu' + Vendor='Englander Institute for Precision Medicine' \ + maintainer='als2076@med.cornell.edu' #=====================# # Install Beacon # #=====================# From f8b8983e7a3c5614b920364c4bf4a3831f16cab7 Mon Sep 17 00:00:00 2001 From: Alexandros Sigaras Date: Wed, 11 Apr 2018 16:25:35 -0400 Subject: [PATCH 2/5] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 531fd78..270b9b2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ # Dockerfile for Beacon -FROM python:2.7.14 +FROM python:2.7.14-stretch #=====================# # Setup Prerequisites # #=====================# @@ -35,4 +35,4 @@ COPY app ${BEACON_DIR} #=====================# # Beacon Startup # #=====================# -CMD /usr/sbin/apache2ctl -D FOREGROUND \ No newline at end of file +CMD /usr/sbin/apache2ctl -D FOREGROUND From 02511bdc56ffe2fa8f101128da136b38f813f5f5 Mon Sep 17 00:00:00 2001 From: Alexandros Sigaras Date: Tue, 2 Apr 2019 13:29:00 -0400 Subject: [PATCH 3/5] updated readme --- README.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 0ea8a4b..85e0c54 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Beacon -[![Docker Automated build](https://img.shields.io/docker/automated/jrottenberg/ffmpeg.svg)](https://hub.docker.com/r/eipm/beacon/) [![Docker Pulls](https://img.shields.io/docker/pulls/eipm/beacon.svg)](https://hub.docker.com/r/elementolab/beacon/) [![Docker Stars](https://img.shields.io/docker/stars/eipm/beacon.svg)](https://hub.docker.com/r/eipm/beacon/) +[![Docker Automated build](https://img.shields.io/docker/automated/jrottenberg/ffmpeg.svg)](https://hub.docker.com/r/eipm/beacon/) [![Docker Pulls](https://img.shields.io/docker/pulls/eipm/beacon.svg)](https://hub.docker.com/r/eipm/beacon/) [![Docker Stars](https://img.shields.io/docker/stars/eipm/beacon.svg)](https://hub.docker.com/r/eipm/beacon/) [![Maintainability](https://api.codeclimate.com/v1/badges/b3607af6a3051d8df2eb/maintainability)](https://codeclimate.com/github/eipm/beacon/maintainability) [![Deploy to Azure](http://azuredeploy.net/deploybutton.png)](https://azuredeploy.net/) @@ -13,8 +13,8 @@ This project is an open source dockerized automated build implementation of the GA4GH Beacon, enabling researchers to light their own beacon with a single command line. -[Github Project](https://github.com/eipm/beacon) -[Docker Automated Build](https://hub.docker.com/r/eipm/beacon/) +- [Github Project](https://github.com/eipm/beacon) +- [Docker Automated Build](https://hub.docker.com/r/eipm/beacon/) ## About Beacon @@ -22,8 +22,8 @@ The Beacon Project is a simple, open web service that balances the desire of int ### Beacon Resources -[Beacon Project Home Page](http://ga4gh.org/#/beacon) -[Beacon on Github](https://github.com/maximilianh/ucscBeacon) +- [Beacon Project Home Page](http://ga4gh.org/#/beacon) +- [Beacon on Github](https://github.com/maximilianh/ucscBeacon) ## About Docker @@ -31,8 +31,8 @@ Docker is an open-source project that automates the deployment of applications i ### Docker Resources -[Docker Home Page](https://www.docker.com) -[Docker Run Reference](https://docs.docker.com/engine/reference/run/) +- [Docker Home Page](https://www.docker.com) +- [Docker Run Reference](https://docs.docker.com/engine/reference/run/) ## Launch a test Beacon @@ -50,7 +50,7 @@ eipm/beacon ## Creating your own configuration file -Create your own beacon.conf file using [this template](https://github.com/ElementoLab/beacon/blob/master/config/beacon.conf). +Create your own beacon.conf file using [this template](https://github.com/eipm/beacon/blob/master/config/beacon.conf). ## Adding your own data and configuration file @@ -73,7 +73,7 @@ eipm/beacon docker run -it --name beacon \ -v my/data/:/data \ -v /my/beacon/conf/beacon.conf:/var/www/html/beacon/beacon.conf \ --p 8080:80 elementolab/beacon /bin/bash +-p 8080:80 eipm/beacon /bin/bash ``` #### B. Run the import dataset command for dataset 'ipm' From b3352923ad21114c7d9264cd7567cd8032e2adfb Mon Sep 17 00:00:00 2001 From: Alexandros Sigaras Date: Tue, 2 Apr 2019 13:29:08 -0400 Subject: [PATCH 4/5] Updated Dockerfile to latest python version --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 270b9b2..4390b9f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ # Dockerfile for Beacon -FROM python:2.7.14-stretch +FROM python:2.7.16-stretch #=====================# # Setup Prerequisites # #=====================# From e254d07ee292f7dc4282f971a25602d3c06c1da7 Mon Sep 17 00:00:00 2001 From: Alexandros Sigaras Date: Tue, 2 Apr 2019 13:31:21 -0400 Subject: [PATCH 5/5] Updated readme --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 85e0c54..090bf9c 100644 --- a/README.md +++ b/README.md @@ -41,7 +41,7 @@ Docker is an open-source project that automates the deployment of applications i ```bash docker run -d --name "beacon" \ ---restart=always \ +--restart on-failure:5 \ -p 8080:80 \ eipm/beacon ``` @@ -54,18 +54,18 @@ Create your own beacon.conf file using [this template](https://github.com/eipm/b ## Adding your own data and configuration file -### 1. Run a beacon with your own SQLite DB and configuration file. +### 1. Run a beacon with your own SQLite DB and configuration file ```bash docker run -d --name "beacon" \ ---restart=always \ +--restart on-failure:5 \ -p 8080:80 \ -v my/database/path/beaconData.GRCh37.sqlite:/var/www/html/beacon/ucscBeacon/beaconData.GRCh37.sqlite \ -v /my/beacon/conf/beacon.conf:/var/www/html/beacon/beacon.conf \ eipm/beacon ``` -### 2. Run a beacon in interactive mode and import your own data and configuration file. +### 2. Run a beacon in interactive mode and import your own data and configuration file #### A. Launch Beacon with your data