dockerize_platypus

Dockerize report_html_db.pl result and upload for docker cloud

Installing dependencies

Wendellor's package was made using Python3. So you will need to execute some commands:

sudo apt-get install git \
    python-dev\
    python-pip\
    python3-dev\
    python3-pip

Here you're installing:

Package	Description
git	Version control system for tracking changes in computer files and coordinating work on those files among multiple people. In this case, for manage our repository
python-dev	Header files, a static library and development tools for building Python modules, extending the Python 2.7 interpreter or embedding Python 2.7 in applications.
python-pip	pip is the Python 2.7 package installer. It integrates with virtualenv, doesn't do partial installs, can save package state for replaying, can install from non-egg sources, and can install from version control repositories.
python3-dev	Header files, a static library and development tools for building Python modules, extending the Python 3 interpreter or embedding Python 3 in applications.
python3-pip	pip is the Python 3 package installer. It integrates with virtualenv, doesn't do partial installs, can save package state for replaying, can install from non-egg sources, and can install from version control repositories.

You'll need to install EGene2 platform and Docker

Install

You can install this project with the following command:

sudo pip3 install git+https://github.com/WendelHime/dockerize_platypus.git

Upgrade

Upgrade with the following command:

sudo pip3 install --upgrade Dockerize-Platypus

Uninstalling

Uninstall with the following command:

sudo pip3 uninstall Dockerize-Platypus

Running an example

Here we're going to execute dockerize_platypus.py and see how it works.

Copy example files

Copy examples file after install:

cp -r /usr/share/dockerize_platypus/example example
cd example

If you haven't installed with sudo, please, clone this repository and access example files:

git clone https://github.com/WendelHime/dockerize_platypus.git
cd dockerize_platypus/example

Preparing data EGene2

First of all, we need to build our database, I'll not explain how EGene2 works or the components inside the example configuration file, so please, take your time and read!

You're going to run something like:

bigou_m.pl -c evidence.conf -d minibct_db -u chadouser -p egene_chado -h localhost -o output_dir

After finish, take a look of report_html_db.conf and change paths, after that, you can execute this configuration, samething as above:

bigou_m.pl -c report_html_db.conf -d minibct_db -u chadouser -p egene_chado -h localhost -o output_dir

Running dockerize_platypus

After report_html_db.conf finish, we can dockerize this result using:

dockerize_platypus.py Minibacteria output chadouser minibct_db egene_chado wendelhime

If didn't understant anything:

dockerize_platypus.py -h
usage: dockerize_platypus.py [-h] [-v] [--log LOG]
                             organism filepath dbuser dbname dbpass
                             docker_user

dockerize_platypus.py - dockerize report_html_db.pl result

positional arguments:
  organism       Organism name for docker tag
  filepath       Output filepath from report_html_db.pl
  dbuser         DB username
  dbname         DB name
  dbpass         DB password to be used on docker
  docker_user    Docker username

optional arguments:
  -h, --help     show this help message and exit
  -v, --version  show program's version number and exit
  --log LOG      output filepath log

Creates a docker image based on report_html_db.pl, build it and push into
docker cloud