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Merge pull request #510 from ngeorges-cnrs/packaging_doc
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Update application packaging doc.
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axlbonnet authored Dec 9, 2024
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<link rel="StyleSheet" href="../css/doc_main.css" type="text/css" />
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<a name="contents"></a><h1>How to import an application</h1>

<h2><a name="docker"></a>Write your application descriptor with Boutiques</h2>
<p>Applications are imported into VIP using <a href="https://github.com/boutiques/boutiques" target="_blank">Boutiques</a> descriptors.</p>

<p>Please do not hesitate to contact us if you need help with writing your application descriptor.
Once the descriptor is ready, VIP admins will import it for you.</p>

<p>We recommend that descriptors are versionned and published to Zenodo, similarly to what has been done for the Gate OpenDose application:</p>
<ul>
<li><a href="https://github.com/CISI-INSERM/OpenDose-Computing/blob/master/Boutiques/gate-opendose-descriptor-docker.json" target="_blank">Example of descriptor on github</a></li>
<li><a href="https://zenodo.org/record/2573071" target="_blank">Example of descriptor on Zenodo</a></li>
</ul>

<p>Note that publising to Zenodo can be done through VIP, once the application is imported with its Boutiques descriptor. In exchange,
you will get a DOI allowing for the proper citation of the application. </p>

<p>We also recommend that you use containers (such as Docker or Singularity) to facilitate application installation and sharing.</p>


<h2><a name="docker"></a>Docker guidelines</h2>
<ul>
<li>If you are not familiar with Docker, <a href="https://docs.docker.com/engine/getstarted/" target="_blank">read the docs</a> on the Docker website.</li>
<li>We recommend to build containers from a <a href="https://docs.docker.com/engine/reference/builder" target="_blank">Dockerfile</a>.</li>
<li>For efficient management of containers in VIP, we recommend that containers use the following images if possible:
<ul>
<li>Linux distribution: <a href="https://hub.docker.com/r/_/centos/" target="_blank">centos7</a> (official).</li>
<li>Compiled Matlab applications: <a href="https://hub.docker.com/r/viplatform/matlab-compiler-runtime" target="_blank">viplatform/matlab-compiler-runtime</a> (unofficial).</li>
<li>Applications using <a href="https://github.com/MRtrix3/mrtrix3" target="_blank">MRtrix3</a>: <a href="https://hub.docker.com/r/glatard/mrtrix3/" target="_blank">glatard/mrtrix3</a> (unofficial).</li>
</ul>
</li>
<li>Compiled applications: avoid using architecture-specific
compilation flags as it will produce non-portable code
(<code>Illegal instruction</code> error messages).</li>
<li>Your application is supposed to work with a regular user (not as root).</li>
</ul>
<br/>


<h2><a name="troubleshooting"></a>Troubleshooting tips: compiled Matlab functions</h2>
Arguments of compiled Matlab functions will be passed as strings, which may create nasty
bugs at runtime. We recommend that numerical arguments are handled using code such as:
<pre>
<code>
if ~isnumeric(parameter)
parameter = str2double(parameter);
if isnan(parameter)
disp('The parameter value is not a number')
return
end
end
</code>
</pre>
<br/>


<p>See the <a href="https://github.com/virtual-imaging-platform/VIP-portal/wiki/Packaging-guide" target="_blank">Application packaging guide</a>
for instructions on how to get your application packaged, so that it can be imported by VIP admins.</p>
<p>Please do not hesitate to contact us if you need help with your application packaging.</p>
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