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