The Guideline for Container GitHub Respository README.md Creation

The Guideline for Container GitHub Respository README.md Creation

Objectives

• To make sure each container Github repository has its own README.md.
• To make sure each container Github repository follows the structure and same style.
• To be able to reuse README.md for PhenoMeNal App Library without extra inputs.

Guideline

• Please create the README.md in your container's GitHub Repository root level.
• Strictly follow the specification in the next section.
• For quick start, you can use Example Template in the end of this document.

Specification

• Logo: The logo needs have the text "Logo" inside the square bracket place holder to be recognized at the App Library. Example:

![Logo](rNMR_logo.gif)

• Tool name: First single hashtag (#) on the ReadMe.md file will be taken as tool name. Example:

# rNMR

• Version: Should always go after the first hastag and before the second hastag. The line needs to respond to the regexp "^Version: (.+)" being the first group the actual version. This is the version of the tool being containerised. Example:

Version: 1.0.0

Fields

For the App Library, the following fields will be parsed. Examples:

• Short Description This should only be 20 words or less, hopefully a single sentence.

## Short description

Super tool, produces unbelievably exact results even with noisy data.

• Description You can put the tool's paper abstract, or any other description into this section, there is no word limit.

## Description
For a long time, the field of bioinformatics have longed a tool that can deal with data noise while still producing very exact results. Here we present Super tool.... a paragraph of text or so...

• Key features This section provides a list of features about this app. Please add "-" at the front of each feature. Otherwise, README.md will not be parsed properly. Example:

## Key features
- NMR Processing
- MS

• Functionality Please select suitable category from this hierarchy or this Google doc Please add "-" at the front of each item. "/" is as the indication for a child node in a tree. Example:

## Functionality
- Annotation / NMR
- Post-processing

• Approaches Please select suitable category from this hierarchy. Please add "-" at the front of each item. "/" is as the indication for a child node in a tree.

## Approaches
- Metabolomics / Targeted

• Instrument Data Types Please select suitable category from this hierarchy or this Goolge doc. Please add "-" at the front of each item. "/" is as the indication for a child node in a tree.

## Instrument Data Types
- NMR / 1D NMR
- NMR / 2D NMR / 2D TOCSY
- NMR / 1H NMR

• Screenshots: The screenshot needs have the text "screenshot" inside the square bracket place holder to be recognized at the App Library.

## Screenshots
![screenshot](screenshots/s1.gif)
![screenshot](screenshots/s2.gif)

• Tool Authors: Please add "-" at the front of each item. Authors or affiliations can be hyperlinked as usual using [Text](http://example.link.org/person) structure, or it can be left unlinked. Example:

## Tool Authors 
- Ian A. Lewis (University of Calgary)
- Seth C. Schommer (Wisconsin-Madison University and Sunquest Information Systems)
- [Author 2](link_to_author_2) (affiliation)

• Container Contributors: Please add "-" at the front of each item. Again, contributors can be hyperlinked as described for authors, or be left as simple text.

## Container Contributors
- [Kristian Peters](https://github.com/korseby) (IPB Halle)
- [Contributor 2](link_to_contributior_2) (affiliation)

• Website: Please add "-" at the front of each item. Do not explicitly hyperlink please, just leave as text. Example:

## Website
- http://rnmr.nmrfam.wisc.edu/

• Git Repository: Please add "-" at the front of each item. Again, do not explicitly hyperlink.

## Git Repository
- https://github.com/phnmnl/container-rnmr.git

• Installation: Free text with triple tick code blocks, comprising docker, ipython and galaxy usage.

## Installation 

triple`
docker pull ...
triple`

• Usage Instruction: Free text with triple tick code blocks, comprising docker, ipython and galaxy usage.

## Usage Instructions

• Publications: Use AMA style publications as a list (you can export AMA from PubMed, on the Formats: Citation link when looking at the entry). IMPORTANT! Publication section must be at the end and cannot be empty.

## Publications
- Lewis IA, Schommer SC, Markley JL. rNMR: open source software for identifying and quantifying metabolites in NMR spectra. Magnetic Resonance in Chemistry . 2009;47(S1):S123-S126. doi:10.1002/mrc.2526.

Point of Contact

• Upon the completion of your container README.md, please send the URL of your container GitHub Repository to Marco Enrico Piras
• Please feel free to contact Marco Enrico Piras if you have any question regarding the creation of README.md.

Example Template

• An example template can be found from the README.md of rNMR (https://github.com/phnmnl/container-rnmr/blob/master/README.md)