cgenomics/karyon repository overview

⁠Karyon Docker

To-Do A one paragraph description about the container.

⁠Getting Started (To-Do)

If you haven't done so already, you'll need to "Clone or Download" this project.

git clone https://github.com/Gabaldonlab/karyon_docker.git

⁠Prerequisities

In order to run this container you'll need docker installed.

• Linux⁠

In addition, to work with the Karyon shell script menu it's necessary to install "dialog command". The dialog command (https://bash.cyberciti.biz/guide/Bash_display_dialog_boxes⁠) allows you to display a variety of questions or display messages using dialog boxes from a shell script.

sudo apt-get update
sudo apt-get install dialog

⁠Usage (To-Do)

In order to start to work with Karyon Docker you can do it within the shell script menu (Beginner Docker user) or directly with Docker commands (Advanced Docker user).

To use the shell script menu type:

sh menu.sh

These are the basic commands to work with Karyon Docker.(???)

⁠Building a new image

Building your docker container will take a few minutes the first time through. If you change your script or Dockerfile and need to rebuild, the subsequent times will be faster, since Docker builds things in layers.

docker build -t cgenomics/karyonpip:1.0 .

⁠Testing a new image (???)

⁠Running the image

Every time you run a Docker container, it uses the Karyon Docker image to remake it. When the container is closed, everything in it goes away! Also, for every one of those containers you need to name it with an alias.

docker run -dit --name=your-alias -v /your/karyon/location:/root/src/karyon/shared --rm cgenomics/karyonpip:1.0`" 0 0;;

⁠Launch Karyon script

docker exec -w /your/karyon/location/ karyon python scripts/karyon.py -l shared/your-data-file-one shared/your-data-file-two... -d shared/output -T

⁠Interactive session in a Karyon container

To start an interactive session in a container first you need to run the image with an alias.

docker exec -it your-alias /bin/bash

⁠Stoping a container

docker stop your-alias

⁠Removing a container

docker rm your-alias

⁠Showing running containers

docker ps

⁠Showing images

docker images

⁠Container Parameters (To-Do)

List the different parameters available to your container

⁠Shared volume

• /your/karyon/location/ - File location

⁠Useful File Locations

• /your/karyon/location/shared - Folder to share data with the container

• /your/karyon/location/src/dependencies - Folder with programs used by Karyon script

⁠Built With

(To-Do)

• List the software v0.1.3
• And the version numbers v2.0.0
• That are in this container v0.3.2

⁠Find Us

(To-Do)

• GitHub⁠

⁠Support

(To-Do)

If you have any issues or doubts, please send an email to ....

⁠Authors

(To-Do)

• Miguel Ángel Naranjo Ortiz - Pipeline work - MANaranjo⁠
• Manuel Molina Marín - Docker work - manumolina⁠

⁠License

(To-Do)

This project is licensed under the MIT License - see the LICENSE.md⁠ file for details.