view massPix @ 0:dada1f17021d draft

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date Tue, 24 Sep 2019 04:37:32 -0400
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        <article class="markdown-body entry-content p-5" itemprop="text"><h1><a id="user-content-masspix-for-galaxy" class="anchor" aria-hidden="true" href="#masspix-for-galaxy"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>massPix for Galaxy</h1>
<p>This is Galaxy tool for R package <code>massPix</code> which processes high resolution
mass spectrometry imaging data, performs multivariate statistics (PCA,
clustering) and lipid identification. For details, see
<a href="https://github.com/hallz/massPix">R package massPix</a> and <a href="https://link.springer.com/article/10.1007%2Fs11306-017-1252-5" rel="nofollow">Metabolomics
publication</a>.</p>
<h2><a id="user-content-installation" class="anchor" aria-hidden="true" href="#installation"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Installation</h2>
<ul>
<li>
<p>Install <a href="https://github.com/galaxyproject/galaxy">Galaxy</a> under Linux.</p>
</li>
<li>
<p>Install <a href="https://docs.conda.io/en/latest/miniconda.html" rel="nofollow">conda</a> under
Linux. <code>conda</code> is used to install <code>requirements</code> of this tool.</p>
</li>
<li>
<p>Use <code>git</code> to clone this tool</p>
<div class="highlight highlight-source-shell"><pre>git clone https://github.com/wanchanglin/massPix.git</pre></div>
</li>
<li>
<p>Add this tool's location into Galaxy' tool config file:
<code>~/Galaxy/config/tool_conf.xml</code>. For example, one simplified
<code>tool_conf.xml</code> looks like:</p>
<div class="highlight highlight-text-xml"><pre>&lt;?<span class="pl-ent">xml</span><span class="pl-e"> version</span>=<span class="pl-s"><span class="pl-pds">'</span>1.0<span class="pl-pds">'</span></span><span class="pl-e"> encoding</span>=<span class="pl-s"><span class="pl-pds">'</span>utf-8<span class="pl-pds">'</span></span>?&gt;
&lt;<span class="pl-ent">toolbox</span> <span class="pl-e">monitor</span>=<span class="pl-s"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span>&gt;
  
  &lt;<span class="pl-ent">section</span> <span class="pl-e">id</span>=<span class="pl-s"><span class="pl-pds">"</span>getext<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>Get Data<span class="pl-pds">"</span></span>&gt;
    &lt;<span class="pl-ent">tool</span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>data_source/upload.xml<span class="pl-pds">"</span></span> /&gt;
  &lt;/<span class="pl-ent">section</span>&gt;
  
  &lt;<span class="pl-ent">section</span> <span class="pl-e">id</span>=<span class="pl-s"><span class="pl-pds">"</span>MyTools<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>My Tools<span class="pl-pds">"</span></span>&gt;
    &lt;<span class="pl-ent">tool</span> <span class="pl-e">file</span>=<span class="pl-s"><span class="pl-pds">"</span>/path/to/massPix/massPix.xml<span class="pl-pds">"</span></span> /&gt;
  &lt;/<span class="pl-ent">section</span>&gt;

&lt;/<span class="pl-ent">toolbox</span>&gt;</pre></div>
</li>
<li>
<p>The Galaxy tool uses <a href="https://cran.r-project.org/" rel="nofollow">R</a> packages <code>optparse</code>,
<code>WriteXLS</code>, <code>calibrate</code> and  <code>rJava</code>. This tool embeds a modified
<code>massPix</code> package for Galaxy only.</p>
</li>
<li>
<p>To test the tool, use data inside <code>test-data</code> or download test data (.ibd
and .imzML files) from the
<a href="https://www.ebi.ac.uk/metabolights/" rel="nofollow">MetaboLights</a> repository accession
number <a href="https://www.ebi.ac.uk/metabolights/MTBLS487" rel="nofollow">MTBLS487</a>.</p>
</li>
</ul>
<h2><a id="user-content-authors-contributors--contacts" class="anchor" aria-hidden="true" href="#authors-contributors--contacts"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Authors, contributors &amp; contacts</h2>
<ul>
<li>Wanchang Lin (<a href="mailto:wl361@cam.ac.uk">wl361@cam.ac.uk</a>), University of Cambridge</li>
<li>Zoe Hall (<a href="mailto:zlh22@cam.ac.uk">zlh22@cam.ac.uk</a>), University of Cambridge</li>
<li>Julian L Griffin (<a href="mailto:jlg40@cam.ac.uk">jlg40@cam.ac.uk</a>), University of Cambridge</li>
</ul>
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