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README.md
demo.py
sample.fasta
welcome.png

README.md

##Setting up a GitHub repository

####Here is how you can set up a GitHub repository.

  1. Let's say you have a folder containing the differents elements you want to provide for the ARTBio test.
  • A memo named README.md which will be integrated by GitHub as the description of this repositrory.
  • A screenshot welcome.png of the modified galaxy welcome page.
  • A python script demo.py and a fasta sample sample.fasta to test it
  1. Initialise a local git repository

    git init
  2. Commit the differents files to the newly created local repository

    git add README.md welcome.jpg demo.py sample.fasta
    git commit -m "initializing repository"
  3. From your GitHub account, make a remote repository. Like this one ARTBio-demo

  4. Locally add the URL of the remote repository you just made
    Here we assume your GitHub account already know your computer by his SSH public key. You could use HTTPS protocol instead by adding 'https://github.com/zakrapovic/ARTbio-demo.git'

    git remote add origin git@github.com:zakrapovic/ARTbio-demo.git
  5. Push the content of the local repository to the remote one

    git push -u origin master

####That's all! You just set up a GitHub repository.

##Setting up a Galaxy server

  1. Download galaxy by cloning their GitHub repositry

    git clone https://github.com/galaxyproject/galaxy/
  2. Run it once for initialization

    cd galaxy
    sh run.sh
  3. Open the welcome.html

  4. Here we remove the default message and replace it with a frame containing the artbio website

    replace

    <div class="donemessagelarge">
        <p><strong>Your Galaxy is running!</strong></p>
        <hr>
        <ul>
            <li>To learn how to use Galaxy please see the <a href="https://wiki.galaxyproject.org/Learn">wiki</a></li>
            <li>To install new tools to your Galaxy follow the <a href="https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial">tutorial</a></li>
            <li>To set up your Galaxy for others to use please read <a href="https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer">this</a></li>
        </ul>
        <p><h5>Thank you for trying Galaxy.</h5></p>
    </div>

    by

    <iframe src="https://mississippi.snv.jussieu.fr/artbio/" width="800" height="900" align="center"></iframe>
    <p><strong>You just put a website inside a website</strong></p>
    <div class="donemessagelarge">
        <p><h5>Thank you for considering my application.</h5></p>
    </div>
  5. Restart the server

####That's all! You just downloaded, customized, and started a Galaxy server

ARTbio Logo