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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/ivar">Debian Med / ivar</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/a05e6ab556eba22a5f86c4b36a4335e4a85cda89">a05e6ab5</a></strong>
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<span>by Pranav Ballaney</span>
<i>at 2020-06-17T06:04:02+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch to include local file to avoid lintian warning
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<h4>3 changed files:</h4>
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<a href="#c0b4426ffc6c4557f35032801af9a0836a8e6cb3">
debian/ivar-doc.install
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<a href="#5f7b18dee983584e49a2de1ce4314b1de90e9c47">
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patches/fix_pipeline_link.patch
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patches/series
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<h4>Changes:</h4>
<li id="c0b4426ffc6c4557f35032801af9a0836a8e6cb3">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/a05e6ab556eba22a5f86c4b36a4335e4a85cda89#c0b4426ffc6c4557f35032801af9a0836a8e6cb3"><strong>debian/ivar-doc.install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">docs</span><span class="o" style="font-weight: 600;">/</span><span class="nx">html</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">ivar</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">docs</span><span class="o" style="font-weight: 600;">/</span><span class="nx">html</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">ivar</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">pipeline</span><span class="o" style="font-weight: 600;">/</span><span class="nx">pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="nx">png</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">ivar</span><span class="o" style="font-weight: 600;">/</span><span class="nx">html</span><span class="o" style="font-weight: 600;">/</span><span class="nx">pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="nx">png</span></span></pre>
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<li id="5f7b18dee983584e49a2de1ce4314b1de90e9c47">
<a href="https://salsa.debian.org/med-team/ivar/-/commit/a05e6ab556eba22a5f86c4b36a4335e4a85cda89#5f7b18dee983584e49a2de1ce4314b1de90e9c47"><strong>patches/fix_pipeline_link.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/html/cookbookpage.html</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/html/cookbookpage.html</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -73,7 +73,7 @@</span> $(function() {</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> <p>The two pipelines are distributed along with iVar and are present in the<a href="https://github.com/andersen-lab/ivar/tree/master/pipeline">pipeline/</a> and <a href="https://github.com/andersen-lab/ivar/tree/master/pipeline_field">pipeline_field/</a> fodlers respectively.</p></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> <p>For both pipelines, there are four parameters that will have to be set in beginning of the Snakefile.</p></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> <div class="fragment"><div class="line">in_dir = "<input fastq files>"</div><div class="line">out_dir = "<output directory>"</div><div class="line">bed = "<bed-file-with-primer-positions>"</div><div class="line">ref="<path to reference fasta>"</div></div><!-- fragment --><div class="image"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<img src="https://raw.githubusercontent.com/andersen-lab/ivar/master/pipeline/pipeline.png" width="500"/></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<img src="pipeline.png" width="500"/></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </div></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> <h3>Call iSNVs from samples with known reference sequence</h3></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> <p><a href="https://github.com/andersen-lab/paper_2018_primalseq-ivar/blob/master/cookbook/CookBook.ipynb">Link to Jupyter Notebook</a></p></span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/commit/a05e6ab556eba22a5f86c4b36a4335e4a85cda89#3606774169a42ab183e9802974985fbf84881919"><strong>patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fix_pipeline_link.patch</span></pre>
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