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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/unicycler">Debian Med / unicycler</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/9fe0c2d165bf2da19b2b82d7f62616a8763fce8d">9fe0c2d1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-08T13:10:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spades name
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/21f50585c4a0963698df09401d35c7728f4e332e">21f50585</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-08T13:39:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Provide test data in build dir to provide these for build time tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/3f13672ea9a6462fc22f8b2c7864ec89f6ed674c">3f13672e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-08T15:52:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Provide data files and try to fix PYTHONPATH (which does nor work yet)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/664171f3aed30ef28fb95ef13c7ec08a801a8a12">664171f3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-08T15:55:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">building the dynamic library requires extra make call
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/9d9112c7354a58ac38d6167ff87f34e207bb9be2">9d9112c7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-08T16:23:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Provide the dynamic lib for running the test suite
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/a31911a4f4cff486ffa173499cc573c7c46ad7ac">a31911a4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-10T15:21:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add racon to (Build-)Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/12489935ee409dc417a7885cb73ff67af22a6be6">12489935</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-10T15:22:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove object files
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
</span>
</a>
</li>
<li class="file-stats">
<a href="#69079773d30c2f1c57281d76c3dca3a2349807e9">
<span class="new-file">
+
debian/patches/spades.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/unicycler/compare/c2b0d33f5c4cd4e1ec67c8c04e01fd141e3a4d7b...12489935ee409dc417a7885cb73ff67af22a6be6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
<hr>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,14 @@ Build-Depends: debhelper (>= 11~),</td>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
</td>
<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3-all,</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10
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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> spades</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> default-jdk,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> bowtie2,</span>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> freebayes,</span>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> ncbi-blast+,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> racon,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> samtools,</span>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> spades,</span>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> zlib1g-dev</span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Standards-Version: 4.1.4</span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/unicycler</span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/unicycler.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,10 +24,13 @@ Package: unicycler</td>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> spades,</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> ncbi-blast+,</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> default-jre,</span>
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22
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> bowtie2,</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> samtools</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> freebayes,</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> ncbi-blast+,</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> racon,</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> spades</span>
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24
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Description: hybrid assembly pipeline for bacterial genomes</span>
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25
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> Unicycler is an assembly pipeline for bacterial genomes. It can assemble</span>
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26
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> Illumina-only read sets where it functions as a SPAdes-optimiser. It can</span>
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<a href="https://salsa.debian.org/med-team/unicycler/compare/c2b0d33f5c4cd4e1ec67c8c04e01fd141e3a4d7b...12489935ee409dc417a7885cb73ff67af22a6be6#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">spades.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/unicycler/compare/c2b0d33f5c4cd4e1ec67c8c04e01fd141e3a4d7b...12489935ee409dc417a7885cb73ff67af22a6be6#69079773d30c2f1c57281d76c3dca3a2349807e9"><strong>debian/patches/spades.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Fri, 25 May 2018 10:59:36 +0200</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: SPAdes is in Debian at /usr/bin/spades</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test_dependencies.py</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test_dependencies.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -42,7 +42,7 @@ class TestDependencies(unittest.TestCase</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> def test_spades_not_found(self):</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> stdout, stderr, ret_code = self.run_unicycler(['--spades_path', 'not_a_real_path'])</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(bool(re.search(r'spades.py\s+not found', stdout)))</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(bool(re.search(r'spades\s+not found', stdout)))</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> self.assertTrue('could not find SPAdes' in stderr)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> self.assertEqual(ret_code, 1)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -102,14 +102,14 @@ class TestDependencies(unittest.TestCase</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> def test_no_rotate(self):</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> stdout, stderr, ret_code = self.run_unicycler(['--spades_path', 'not_a_real_path',</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> '--no_rotate'])</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(bool(re.search(r'spades.py\s+not found', stdout)))</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(bool(re.search(r'spades\s+not found', stdout)))</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> self.assertTrue(bool(re.search(r'makeblastdb\s+not used', stdout)))</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> self.assertTrue(bool(re.search(r'tblastn\s+not used', stdout)))</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> def test_no_pilon(self):</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> stdout, stderr, ret_code = self.run_unicycler(['--spades_path', 'not_a_real_path',</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> '--no_pilon'])</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(bool(re.search(r'spades.py\s+not found', stdout)))</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(bool(re.search(r'spades\s+not found', stdout)))</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> self.assertTrue(bool(re.search(r'bowtie2-build\s+not used', stdout)))</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> self.assertTrue(bool(re.search(r'bowtie2\s+not used', stdout)))</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> self.assertTrue(bool(re.search(r'samtools\s+not used', stdout)))</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -119,12 +119,12 @@ class TestDependencies(unittest.TestCase</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> def test_verbosity_1(self):</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> stdout, stderr, ret_code = self.run_unicycler(['--spades_path', 'not_a_real_path',</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> '--verbosity', '1'])</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(bool(re.search(r'spades.py\s+not found', stdout)))</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(bool(re.search(r'spades\s+not found', stdout)))</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> self.assertTrue(bool(re.search(r'Program\s+Version\s+Status', stdout)))</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> self.assertFalse(bool(re.search(r'Program\s+Version\s+Status\s+Path', stdout)))</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> def test_verbosity_2(self):</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> stdout, stderr, ret_code = self.run_unicycler(['--spades_path', 'not_a_real_path',</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> '--verbosity', '2'])</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(bool(re.search(r'spades.py\s+not found', stdout)))</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(bool(re.search(r'spades\s+not found', stdout)))</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> self.assertTrue(bool(re.search(r'Program\s+Version\s+Status\s+Path', stdout)))</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/overlap_removal_test.py</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/overlap_removal_test.py</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -94,7 +94,7 @@ def run_spades(out_dir):</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> reads_2 = os.path.join(out_dir, 'reads_2.fastq')</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> reads_unpaired = os.path.join(out_dir, 'reads_unpaired.fastq')</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- spades_cmd = ['spades.py', '-o', out_dir, '--only-assembler', '-k', '21,41,61,81']</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ spades_cmd = ['spades', '-o', out_dir, '--only-assembler', '-k', '21,41,61,81']</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> if os.path.isfile(reads_1):</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> spades_cmd += ['-1', reads_1, '-2', reads_2]</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test_misc.py</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test_misc.py</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -384,14 +384,14 @@ class TestMiscFunctions(unittest.TestCas</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> def test_spades_version_parsing_3(self):</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> spades_version_output = 'option -v not recognized\nSPAdes genome assembler v.3.5.0\n\n' \</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'Usage: SPAdes-3.5.0-Darwin/bin/spades.py [options] ' \</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'Usage: SPAdes-3.5.0-Darwin/bin/spades [options] ' \</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> '-o <output_dir>\n\nBasic options:'</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> version = unicycler.misc.spades_version_from_spades_output(spades_version_output)</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> self.assertEqual(version, '3.5.0')</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> def test_spades_version_parsing_4(self):</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> spades_version_output = 'option -v not recognized\nSPAdes genome assembler v.2.4.0\n\n' \</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'Usage: SPAdes-2.4.0-Darwin/bin/spades.py [options] ' \</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'Usage: SPAdes-2.4.0-Darwin/bin/spades [options] ' \</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> '-o <output_dir>\n\nBasic options:'</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> version = unicycler.misc.spades_version_from_spades_output(spades_version_output)</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> self.assertEqual(version, '2.4.0')</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -93,7 +93,7 @@ Reasons to __not__ use Unicycler:</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> * [ICC](https://software.intel.com/en-us/c-compilers) also works (though I don't know the minimum required version number)</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> * [setuptools](https://packaging.python.org/installing/#install-pip-setuptools-and-wheel) (only required for installation of Unicycler)</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> * For short-read or hybrid assembly:</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * [SPAdes](http://bioinf.spbau.ru/spades) v3.6.2 or later (`spades.py`)</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * [SPAdes](http://bioinf.spbau.ru/spades) v3.6.2 or later (`spades`)</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> * For long-read or hybrid assembly:</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> * [Racon](https://github.com/isovic/racon) (`racon`)</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> * For polishing</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -411,7 +411,7 @@ Run `unicycler --help_all` to see a comp</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> SPAdes assembly:</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> These options control the short-read SPAdes assembly at the beginning of the Unicycler pipeline.</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- --spades_path SPADES_PATH Path to the SPAdes executable (default: spades.py)</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ --spades_path SPADES_PATH Path to the SPAdes executable (default: spades)</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> --no_correct Skip SPAdes error correction step (default: conduct SPAdes error</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> correction)</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> --min_kmer_frac MIN_KMER_FRAC Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -63,7 +63,7 @@ def missing_tool(tool_name):</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> def tool_check():</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> # Check for required programs.</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tools = ['spades.py', 'java', 'pilon', 'samtools', 'bowtie2', 'bowtie2-build',</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tools = ['spades', 'java', 'pilon', 'samtools', 'bowtie2', 'bowtie2-build',</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> 'makeblastdb', 'tblastn']</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> missing_tools = []</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> for tool in tools:</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/unicycler/misc.py</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/unicycler/misc.py</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -124,7 +124,7 @@ def check_spades(spades_path):</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> if not err.decode():</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> quit_with_error('SPAdes was found but does not produce output (make sure to use '</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- '"spades.py" location, not "spades")')</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ '"spades" location, not "spades")')</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> def find_pilon(pilon_path, java_path, args):</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -916,7 +916,7 @@ def spades_path_and_version(spades_path)</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> def spades_version_from_spades_output(spades_output):</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Parses the SPAdes version from the output of spades.py -v</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Parses the SPAdes version from the output of spades -v</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> return re.search(r'v(\d+\.\d+\.\d+)', spades_output).group(1)</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/unicycler/unicycler.py</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/unicycler/unicycler.py</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -320,7 +320,7 @@ def get_arguments():</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> 'These options control the short-read SPAdes '</span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> 'assembly at the beginning of the Unicycler pipeline.'</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> if show_all_args else argparse.SUPPRESS)</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- spades_group.add_argument('--spades_path', type=str, default='spades.py',</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ spades_group.add_argument('--spades_path', type=str, default='spades',</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> help='Path to the SPAdes executable'</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> if show_all_args else argparse.SUPPRESS)</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> spades_group.add_argument('--no_correct', action='store_true',</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -753,7 +753,7 @@ def check_dependencies(args, short_reads</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> spades_path, spades_version, spades_status = '', '', 'not used'</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> else:</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> spades_path, spades_version, spades_status = spades_path_and_version(args.spades_path)</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- spades_row = ['spades.py', spades_version, spades_status]</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ spades_row = ['spades', spades_version, spades_status]</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> if args.verbosity > 1:</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> spades_row.append(spades_path)</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> program_table.append(spades_row)</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -861,7 +861,7 @@ def quit_if_dependency_problem(spades_st</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> quit_with_error('SPAdes cannot run due to an incompatible Python version')</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> if spades_status == 'bad':</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> quit_with_error('SPAdes was found but does not produce output (make sure to use '</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- '"spades.py" location, not "spades")')</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ '"spades" location, not "spades")')</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> if makeblastdb_status == 'not found':</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> quit_with_error('could not find makeblastdb - either specify its location using '</span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> '--makeblastdb_path or use --no_rotate to remove BLAST dependency')</span></pre>
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<a href="https://salsa.debian.org/med-team/unicycler/compare/c2b0d33f5c4cd4e1ec67c8c04e01fd141e3a4d7b...12489935ee409dc417a7885cb73ff67af22a6be6#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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5
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># DEB_SOURCE: the source package name</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM: the package's upstream version</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">export PYBUILD_NAME=unicycler</span>
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14
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># <span class="idiff left right">for hardening you might like to uncomment this:</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"><span class="idiff left right"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># <span class="idiff left right">Build time tests are flaky</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"><span class="idiff left right">export DH_BUILD_MAINT_OPTIONS=nocheck</span></span>
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17
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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18
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">%:</span>
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19
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> echo "Avoid: command 'UnicyclerClean' has no such option 'all'"</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> find . -name "*.o" -delete</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">override_dh_auto_build:</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> dh_auto_build</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> # building the dynamic library requires extra make call</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> make</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">override_dh_auto_test:</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> BUILDPATH=$(shell pybuild --print build_dir --interpreter python3) ; \</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> ln -s $(CURDIR)/sample_data $${BUILDPATH} ; \</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> cp -a unicycler/*.so $${BUILDPATH}/$(PYBUILD_NAME) ; \</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> PYTHONPATH=$${BUILDPATH}/$(PYBUILD_NAME) dh_auto_test</span></pre>
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