Difference between revisions of "Developers Github Guide"
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| − | =Plant Ontology: Developers guide to | + | =Plant Ontology: Developers guide to GitHub access= |
| − | ==Get an account from | + | ==Get an account from GitHub administrator== |
| − | To be granted developer access to the | + | To be granted developer access to the GitHub Plant-ontology repository you need to have a GitHub account and password. Follow on-screen instructions at https://github.com/ |
| − | To get developer access, please email your | + | To get developer access, please email your GitHub username to Justin Elser and by mentioning the following: |
| − | Request for | + | Request for GitHub developers account on: Planteome/plant-ontology/repository |
Your name: | Your name: | ||
Institution: | Institution: | ||
Email address: | Email address: | ||
Office or lab telephone number:(xxx)-xxx-xxxx | Office or lab telephone number:(xxx)-xxx-xxxx | ||
| − | + | GitHub account name: | |
| − | If you already have one, do not worry, it will work. Once you have developer status, start with | + | If you already have one, do not worry, it will work. Once you have developer status, start with the following set of instructions. The terminal you use with vary depending on the type of machine from which you will be using. |
| − | == | + | ==GitHub access via command-line interface== |
| − | If you prefer a command line access via a unix or linux machines, try this. | + | If you prefer a command line access via on a Mac, unix, or linux machines, try this. |
| − | Set up a directory on your | + | Set up a directory on your local computer, with a name of your choice (such as 'plant-ontology': |
<code> | <code> | ||
| − | mkdir ontology | + | mkdir plant-ontology |
| − | cd ontology | + | cd plant-ontology |
</code> | </code> | ||
Get the files by cloning the repository: | Get the files by cloning the repository: | ||
| − | <code>git clone <nowiki>https://github.com/Planteome/plant-ontology.git</nowiki> </code> | + | <code> git clone <nowiki>https://github.com/Planteome/plant-ontology.git</nowiki> </code> |
In order to update an ontology, do this: | In order to update an ontology, do this: | ||
| Line 37: | Line 37: | ||
<code>git pull</code> | <code>git pull</code> | ||
| − | Make your changes to the ontology files, then | + | Make your changes to the ontology files, then stage your modified file to your local repository before committing it. |
<code>git add name_of_file_that_has_been_changed.obo</code> | <code>git add name_of_file_that_has_been_changed.obo</code> | ||
| − | |||
| − | |||
To commit your changes: | To commit your changes: | ||
| Line 54: | Line 52: | ||
<code>git push</code> | <code>git push</code> | ||
| − | It is good practice always to pull a file before revising it. | + | '''It is good practice always to pull a file before revising it.''' |
| + | |||
At any time you can check the status of your local repository vs. the master on Github by typing: | At any time you can check the status of your local repository vs. the master on Github by typing: | ||
| Line 60: | Line 59: | ||
<code>git status</code> | <code>git status</code> | ||
| − | There is a helpful [https://help.github.com/articles/good-resources-for-learning-git-and-github/ guide] on | + | There is a helpful [https://help.github.com/articles/good-resources-for-learning-git-and-github/ guide] on GitHub's help page. |
| + | |||
If you need help in depositing your files, please contact one of us: | If you need help in depositing your files, please contact one of us: | ||
[mailto:jaiswalp@science.oregonstate.edu?Subject=Plantontology%20SVN%20help Pankaj Jaiswal],[mailto:jaiswalp@science.oregonstate.edu?Subject=Plantontology%20SVN%20help Laurel Cooper], [mailto:jaiswalp@science.oregonstate.edu?Subject=Plantontology%20SVN%20help Justin Elser] | [mailto:jaiswalp@science.oregonstate.edu?Subject=Plantontology%20SVN%20help Pankaj Jaiswal],[mailto:jaiswalp@science.oregonstate.edu?Subject=Plantontology%20SVN%20help Laurel Cooper], [mailto:jaiswalp@science.oregonstate.edu?Subject=Plantontology%20SVN%20help Justin Elser] | ||
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===Protégé software=== | ===Protégé software=== | ||
| − | [http://protege.stanford.edu/ Protégé] is a free, open source ontology editor and knowledge-base framework that is useful if you want to | + | [http://protege.stanford.edu/ Protégé] is a free, open source ontology editor and knowledge-base framework that is useful if you want to edit ontologies in RDF(S), OWL, or XML Schema. |
Protégé is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development. | Protégé is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development. | ||
Latest revision as of 21:22, 7 September 2015
Plant Ontology: Developers guide to GitHub access
Get an account from GitHub administrator
To be granted developer access to the GitHub Plant-ontology repository you need to have a GitHub account and password. Follow on-screen instructions at https://github.com/
To get developer access, please email your GitHub username to Justin Elser and by mentioning the following:
Request for GitHub developers account on: Planteome/plant-ontology/repository Your name: Institution: Email address: Office or lab telephone number:(xxx)-xxx-xxxx GitHub account name:
If you already have one, do not worry, it will work. Once you have developer status, start with the following set of instructions. The terminal you use with vary depending on the type of machine from which you will be using.
GitHub access via command-line interface
If you prefer a command line access via on a Mac, unix, or linux machines, try this.
Set up a directory on your local computer, with a name of your choice (such as 'plant-ontology':
mkdir plant-ontology
cd plant-ontology
Get the files by cloning the repository:
git clone https://github.com/Planteome/plant-ontology.git
In order to update an ontology, do this:
git pull
Make your changes to the ontology files, then stage your modified file to your local repository before committing it.
git add name_of_file_that_has_been_changed.obo
To commit your changes:
git commit
This will open your terminal's default text editor (vi, nano, etc...) Enter in your commit message, and save.
To make your committed changes on the Github master, type
git push
It is good practice always to pull a file before revising it.
At any time you can check the status of your local repository vs. the master on Github by typing:
git status
There is a helpful guide on GitHub's help page.
If you need help in depositing your files, please contact one of us: Pankaj Jaiswal,Laurel Cooper, Justin Elser
Ontology editing software:
Obo-Edit software
OBO-Edit is an open source ontology editor written in Java that can be used to browse, search, or edit the PO (or any .obo) files.
OBO-Edit features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities. It is optimized for reading and writing ontologies in the OBO biological ontology file format.
OBO-Edit is developed by the Berkeley Bioinformatics and Open Source Projects, and is funded by the Gene Ontology Consortium.
The latest version of OBO-Edit can be downloaded from SourceForge.
Protégé software
Protégé is a free, open source ontology editor and knowledge-base framework that is useful if you want to edit ontologies in RDF(S), OWL, or XML Schema.
Protégé is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development.
Ontology development
The PO Developers Guide provides details on the standard practices and principles used in development of the Plant Ontology.
