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<h3>
Malihe Asemani pushed to branch master
at <a href="https://salsa.debian.org/med-team/fieldbioinformatics">Debian Med / fieldbioinformatics</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/d8573957d23e20cb916bb33eb62d38120b699f0c">d8573957</a></strong>
<div>
<span>by Malihe Asemani</span>
<i>at 2020-04-09T09:44:26-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding Python to control and rule files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/d959e190a0a1d064dec4c8b75d0a1a28d6c6f053">d959e190</a></strong>
<div>
<span>by Malihe Asemani</span>
<i>at 2020-04-09T10:06:03-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding MIT License explanantion to copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/79328cf4f76c0ed21d886b381db3f498caf090b8">79328cf4</a></strong>
<div>
<span>by Malihe Asemani</span>
<i>at 2020-04-09T10:10:15-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replacing debhelper to debhelper-compat in control file
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</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/ca51297dc37f669b10a826ade80ea9bb2e534477">ca51297d</a></strong>
<div>
<span>by Malihe Asemani</span>
<i>at 2020-04-09T13:05:56-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding python2 to the build and install dep
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</li>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/compare/4cd36dd8c2c193d121e0aa5d392f803529a4fd41...ca51297dc37f669b10a826ade80ea9bb2e534477#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,16 +3,17 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Malihe Asemani <ml.asemani@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<td class="diff-line-num new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (=<span class="idiff left right"> 12)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7" 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="diff-line-num new_line old" data-linenumber="6" 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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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.0</span></span>
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<td class="diff-line-num new old_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="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (=<span class="idiff left right">12), python-all, python-setuptools, python3-all, python3-setuptools, dh-python</span></span>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.3</span></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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/fieldbioinformatics</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">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/fieldbioinformatics.git</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Homepage: https://github.com/artic-network/fieldbioinformatics</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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Package: fieldbioinformatics</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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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num old old_line" data-linenumber="14" 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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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="diff-line-num old old_line" data-linenumber="15" 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="diff-line-num new_line old" data-linenumber="14" 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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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> ${misc:Depends}</span>
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<td class="diff-line-num new old_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="LC14" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<td class="diff-line-num new old_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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<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">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> ${python:Depends},</span>
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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"> ${misc:Depends}</span>
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Description: pipeline for working with virus sequencing data sequenced with nanopore</span>
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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="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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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> This is the ARTIC bioinformatics pipeline for working with virus sequencing</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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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> data, sequenced with nanopore. Nanopore is a complete bioinformatics</span>
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<a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/compare/4cd36dd8c2c193d121e0aa5d392f803529a4fd41...ca51297dc37f669b10a826ade80ea9bb2e534477#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -9,3 +9,20 @@ License: MIT</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Copyright: 2020 Malihe Asemani <ml.asemani@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> Permission is hereby granted, free of charge, to any person obtaining a copy</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> of this software and associated documentation files (the "Software"), to deal</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> in the Software without restriction, including without limitation the rights</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> copies of the Software, and to permit persons to whom the Software is</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> furnished to do so, subject to the following conditions:</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"> The above copyright notice and this permission notice shall be included in all</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> copies or substantial portions of the Software.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> SOFTWARE.</span></pre>
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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">\ No newline at end of file</td>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/compare/4cd36dd8c2c193d121e0aa5d392f803529a4fd41...ca51297dc37f669b10a826ade80ea9bb2e534477#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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="16" 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">@@ -16,9 +16,10 @@ include /usr/share/dpkg/default.mk</td>
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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"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">export PYBUILD_NAME=fieldbioinformatics</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> dh $@<span class="idiff left right"> --with python2,python3 --buildsystem=pybuild</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">#override_dh_auto_test:</span>
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