paulgowdy / GoodDoc

A Template for Clear and Simple Documentation of Bioinformatics Code

GoodDoc -- A Template for Simple and Clear Documentation of Bioinformatics Code!

Please cite our work -- here is the ICMJE Standard Citation:

...and a link to the DOI:

Awesome Logo

You can make a free DOI with zenodo

Website (if applicable)

Intro statement

What's the problem?

Why should we solve it?

What is ?

Overview Diagram

How to use

Installation options:

We provide two options for installing : Docker or directly from Github.

Docker

The Docker image contains as well as a webserver and FTP server in case you want to deploy the FTP server. It does also contain a web server for testing the main website (but should only be used for debug purposes).

1. docker pull ncbihackathons/<this software> command to pull the image from the DockerHub
2. docker run ncbihackathons/<this software> Run the docker image from the master shell script
3. Edit the configuration files as below

Installing from Github

1. git clone https://github.com/NCBI-Hackathons/<this software>.git
2. Edit the configuration files as below
3. sh server/<this software>.sh to test
4. Add cron job as required (to execute .sh script)

Configuration

Examples here

Testing

We tested four different tools with . They can be found in server/tools/ .

Additional Functionality

DockerFile

comes with a Dockerfile which can be used to build the Docker image.

1. git clone https://github.com/NCBI-Hackathons/<this software>.git
2. cd server
3. docker build --rm -t <this software>/<this software> .
4. docker run -t -i <this software>/<this software>

Website

There is also a Docker image for hosting the main website. This should only be used for debug purposes.

1. git clone https://github.com/NCBI-Hackathons/<this software>.git
2. cd Website
3. docker build --rm -t <this software>/website .
4. docker run -t -i <this software>/website