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<h3>
Mattia Rizzolo pushed to branch master
at <a href="https://salsa.debian.org/med-team/porechop">Debian Med / porechop</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/porechop/commit/496802d26281f38d61314a552f0e68657439f8b2">496802d2</a></strong>
<div>
<span>by Mattia Rizzolo</span>
<i>at 2018-09-27T09:44:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Properly use the dh_python3 options to override its behaviour, instead of being clever with it.
For the "strange reason", it's just so to be able to store multiple
variants of a the same (compiled) python module, but this is not the
case here, so just use --no-ext-rename...
Gbp-Dch: Short
Signed-off-by: Mattia Rizzolo <mattia@debian.org>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/porechop/commit/435599ad73616b8f24e0c75fcbbacfa21ca3e75d">435599ad</a></strong>
<div>
<span>by Mattia Rizzolo</span>
<i>at 2018-09-27T09:46:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build only for the default Python3 version.
The software can't cope with being placed in odd places, so can't use
the multiple python version support that Debian has.
Signed-off-by: Mattia Rizzolo <mattia@debian.org>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/porechop/commit/006d4201771d8e9af9277123814d7c7122fc30bd">006d4201</a></strong>
<div>
<span>by Mattia Rizzolo</span>
<i>at 2018-09-27T09:49:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build the package using pybuild.
+ Move all the files to the usual location for Python3 software.
+ Install the entry point directly in /usr/bin instead of symlinking.
+ Explicitly disable the tests (that before weren't even tried).
Signed-off-by: Mattia Rizzolo <mattia@debian.org>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/porechop/commit/9960e83151462f43c377c978edd69b7030d2c1e7">9960e831</a></strong>
<div>
<span>by Mattia Rizzolo</span>
<i>at 2018-09-27T09:50:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set Rules-Requires-Root:no.
Signed-off-by: Mattia Rizzolo <mattia@debian.org>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/porechop/commit/4ed01c43cf81cbf9c1eff0f4d4fa2a7fc4f19b9e">4ed01c43</a></strong>
<div>
<span>by Mattia Rizzolo</span>
<i>at 2018-09-27T09:52:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Changelog for 0.2.3+dfsg-2
Signed-off-by: Mattia Rizzolo <mattia@debian.org>
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
debian/install
</a>
</li>
<li class="file-stats">
<a href="#8349ebd0c596ef9478eb284b6a482b10861b7531">
<span class="deleted-file">
−
debian/links
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/porechop/compare/ccbae5050ac12c0373bbc51691be58c6aaad2284...4ed01c43cf81cbf9c1eff0f4d4fa2a7fc4f19b9e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">porechop (0.2.3+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Properly use the dh_python3 options to override its behaviour, instead</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> of being clever with it.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Build only for the default Python3 version.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> The software can't cope with being placed in odd places, so can't use</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> the multiple python version support that Debian has.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Build the package using pybuild.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> + Move all the files to the usual location for Python3 software.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> + Install the entry point directly in /usr/bin instead of symlinking.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> + Explicitly disable the tests (that before weren't even tried).</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Set Rules-Requires-Root:no.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> -- Mattia Rizzolo <mattia@debian.org> Thu, 27 Sep 2018 11:49:55 +0200</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">porechop (0.2.3+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * Initial release (Closes: #890112)</span>
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<a href="https://salsa.debian.org/med-team/porechop/compare/ccbae5050ac12c0373bbc51691be58c6aaad2284...4ed01c43cf81cbf9c1eff0f4d4fa2a7fc4f19b9e#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,18 +6,20 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python3-all-dev,</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> libseqan2-dev</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> libseqan2-dev,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3-dev,</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python3-setuptools</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Standards-Version: 4.2.1</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/porechop</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/porechop.git</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: https://rrwick.github.io/Porechop</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Package: porechop</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Depends: ${<span class="idiff left right">shlibs</span>:Depends},</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> ${<span class="idiff left right">misc</span>:Depends},</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> ${<span class="idiff left right">python3</span>:Depends}</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Depends: ${<span class="idiff left right">misc</span>:Depends},</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> ${<span class="idiff left right">python3</span>:Depends},</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> ${<span class="idiff left right">shlibs</span>:Depends}</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Description: adapter trimmer for Oxford Nanopore reads</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> Porechop is a tool for finding and removing adapters from Oxford</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> Nanopore reads. Adapters on the ends of reads are trimmed off, and</span>
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<a href="https://salsa.debian.org/med-team/porechop/compare/ccbae5050ac12c0373bbc51691be58c6aaad2284...4ed01c43cf81cbf9c1eff0f4d4fa2a7fc4f19b9e#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">porechop/*.py usr/lib/porechop/porechop</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">porechop/*.so usr/lib/porechop/porechop</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">porechop-runner.py usr/lib/porechop</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">porechop-runner.py usr/bin</span></pre>
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<a href="https://salsa.debian.org/med-team/porechop/compare/ccbae5050ac12c0373bbc51691be58c6aaad2284...4ed01c43cf81cbf9c1eff0f4d4fa2a7fc4f19b9e#8349ebd0c596ef9478eb284b6a482b10861b7531"><strong>debian/links</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/lib/porechop/porechop-runner.py usr/bin/porechop</span></pre>
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<a href="https://salsa.debian.org/med-team/porechop/compare/ccbae5050ac12c0373bbc51691be58c6aaad2284...4ed01c43cf81cbf9c1eff0f4d4fa2a7fc4f19b9e#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,15 +4,15 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># FIXME - never enabled, tests fail, to be investigated</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">export PYBUILD_DISABLE=test</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> dh $@ --with python3</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> dh $@ --with python3<span class="idiff left right"> --buildsystem pybuild</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">override_dh_python3:</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> dh_python3</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> # for some very strange reason dh_python3 is renaming cpp_functions.so to cpp_functions.cpython-36m-$(DEB_SOURCE).so</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> # Just revert this!</span>
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<td class="diff-line-num old old_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> mv debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/$(DEB_SOURCE)/cpp_functions*.so debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/$(DEB_SOURCE)/cpp_functions.so</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> # Did everything worked???</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> find . -name "*.so"</span></pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> dh_python3 --no-ext-rename</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">override_dh_install:</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> dh_install</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> mv -v debian/porechop/usr/bin/porechop-runner.py debian/porechop/usr/bin/porechop</span></pre>
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