deployment scripts for ansible and docker, doc and draft of test in p…

…revision of .travis.yml

README.md

@@ -1 +1,32 @@
-# metavisitor
+# metavisitor
+
+This is the repository for the automated deployment of a [Metavisitor](https://doi.org/10.1371/journal.pone.0168397) Galaxy server
+
+## Quick Start
+
+Tested on Ubuntu 14.04 - You must have root access (be sudoer)
+
+- Install git
+```
+apt-get -y update && apt-get -y install git
+```
+- Clone locally this repository
+```
+git clone https://github.com/ARTbio/metavisitor.git
+```
+- Navigate to metavisitor directory
+```
+cd metavisitor
+```
+
+### For a ansible deployment of metavisitor
+- run the `install.sh` script
+```
+sh install.sh
+```
+### For a Docker image built
+- run the `build_docker_image.sh` script
+```
+sh build_docker_image.sh
+```
+

build_docker_image.sh

@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+set -e
+apt-get install -y python-pip python-dev python-setuptools git htop
+echo "Upgrading pip to v 1.9"
+pip install -U pip
+pip --version
+/usr/local/bin/pip install ansible==2.2
+ansible --version
+
+git clone https://github.com/ARTbio/GalaxyKickStart.git
+rm -rf GalaxyKickStart/Dockerfile GalaxyKickStart/Dockerfile.test
+mv Dockerfile Dockerfile.test GalaxyKickStart/
+rm -rf GalaxyKickStart/group_vars/metavisitor GalaxyKickStart/group_vars/test 
+mv group_vars/metavisitor group_vars/test GalaxyKickStart/group_vars/
+rm -rf GalaxyKickStart/extra-files/metavisitor GalaxyKickStart/extra-files/test
+mv extra-files/metavisitor extra-files/test GalaxyKickStart/extra-files/
+rm -rf GalaxyKickStart/inventory_files/*
+mv inventory_files/metavisitor inventory_files/test GalaxyKickStart/inventory_files/
+
+cd GalaxyKickStart/
+ansible-galaxy install -r requirements_roles.yml -p roles/ -f
+echo "Editing group_vars/all"
+sed -i -e 's/galaxy_manage_trackster: true/galaxy_manage_trackster: false/' group_vars/all
+docker build -t metavisitor .

install.sh

@@ -21,9 +21,10 @@ cd GalaxyKickStart/
 ansible-galaxy install -r requirements_roles.yml -p roles/ -f
 echo "Editing group_vars/all"
 sed -i -e 's/galaxy_manage_trackster: true/galaxy_manage_trackster: false/' group_vars/all
-ansible-playbook -i inventory_files/test galaxy.yml
+ansible-playbook -i inventory_files/metavisitor galaxy.yml
 echo "Sleeping 15 sec before restarting Metavisitor Test Galaxy server"
 echo "zzzz zzzz..."
 sleep 15
 supervisorctl restart galaxy:
-echo "if galaxy:galaxy_web failed to restart with error termination, just do `killall uwsgi; supervisorctl restart galaxy:`"
+sleep 15
+supervisorctl status

test.sh

@@ -0,0 +1,34 @@
+#!/usr/bin/env bash
+set -e
+apt-get install -y python-pip python-dev python-setuptools git htop
+echo "Upgrading pip to v 1.9"
+pip install -U pip
+pip --version
+/usr/local/bin/pip install ansible==2.2
+ansible --version
+
+git clone https://github.com/ARTbio/GalaxyKickStart.git
+rm -rf GalaxyKickStart/Dockerfile GalaxyKickStart/Dockerfile.test
+mv Dockerfile Dockerfile.test GalaxyKickStart/
+rm -rf GalaxyKickStart/group_vars/metavisitor GalaxyKickStart/group_vars/test 
+mv group_vars/metavisitor group_vars/test GalaxyKickStart/group_vars/
+rm -rf GalaxyKickStart/extra-files/metavisitor GalaxyKickStart/extra-files/test
+mv extra-files/metavisitor extra-files/test GalaxyKickStart/extra-files/
+rm -rf GalaxyKickStart/inventory_files/*
+mv inventory_files/metavisitor inventory_files/test GalaxyKickStart/inventory_files/
+
+cd GalaxyKickStart/
+ansible-galaxy install -r requirements_roles.yml -p roles/ -f
+echo "Editing group_vars/all"
+sed -i -e 's/galaxy_manage_trackster: true/galaxy_manage_trackster: false/' group_vars/all
+ansible-playbook -i inventory_files/test galaxy.yml
+echo "Sleeping 15 sec before restarting Metavisitor Test Galaxy server"
+echo "zzzz zzzz..."
+sleep 15
+supervisorctl restart galaxy:
+sleep 15
+supervisorctl status
+
+service supervisor stop
+sleep 5
+docker build -t metavisitor -f Dockerfile.test .