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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/cmdock">Debian Med / cmdock</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256">e298446b</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-06-06T22:03:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Initial packaging
</pre>
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<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
<span class="new-file">
+
debian/changelog
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</li>
<li class="file-stats">
<a href="#2a5743e908a8f3a16d275e2c53a8a4fa78ae86f6">
<span class="new-file">
+
debian/cmdock.install
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
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debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
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debian/copyright
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<li class="file-stats">
<a href="#7ef1b627993b64c5dae251ea3c9df445df15d006">
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debian/libcmdock0.install
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<li class="file-stats">
<a href="#f871d7525a5d14815942d2eaa525f7174af6d238">
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debian/patches/installdir.patch
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<li class="file-stats">
<a href="#be445773d38b48f6f98e814a57b89a3e7151bcef">
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debian/patches/noPCGtest.patch
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<li class="file-stats">
<a href="#75530a216b34342639a71cc6c2be7fdc37b3d77b">
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debian/patches/pythonVersion.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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debian/patches/series
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
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debian/rules
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<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
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debian/salsa-ci.yml
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debian/source/format
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debian/upstream/metadata
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debian/watch
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">cmdock (0.1.3-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #989535)</span>
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<td class="new_line diff-line-num new" data-linenumber="4" 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="LC4" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="5" 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="LC5" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Sun, 06 Jun 2021 19:20:43 +0200</span></pre>
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<br>
</li>
<li id="2a5743e908a8f3a16d275e2c53a8a4fa78ae86f6">
<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#2a5743e908a8f3a16d275e2c53a8a4fa78ae86f6"><strong>debian/cmdock.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2" 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="LC2" class="line" lang="php"><span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span></span></pre>
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</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: cmdock</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Uploaders: Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> meson,</span>
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<td class="new_line diff-line-num new" 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"> libcxxopts-dev,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> libpcg-cpp-dev,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> googletest <!nocheck></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Homepage: https://sidock.si</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/cmdock</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/cmdock.git</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Rules-Requires-Root: no</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">Package: cmdock</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Architecture: any</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends},</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Recommends: python3,</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> perl</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Suggests: tcsh</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Description: fit chemical compounds to proteins and nucleotides</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> This tool for molecular docking / in silico drug screening is a</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> derivative of rDock and the core to the SiDock@Home project to</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> find inhibitors of the SARS-CoV-2 virus.</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Package: libcmdock0</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Suggests: cmdock</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Description: library of cmdock</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> cmdock performs docking / in silico drug screening as a</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> derivative of rDock and is core to the SiDock@Home project to</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> find inhibitors of the SARS-CoV-2 virus.</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> This package provides its shared library.</span></pre>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Name: cmdock</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Source: </span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Files: *</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Copyright: 1998-2006 RiboTargets (subsequently Vernalis (R&D) Ltd)</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> 2006-2012 University of York</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> 2012-2014 University of Barcelona</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> 2019-2020 RxTx</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">License: LGPL-3.0+</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Files: include/indicators/termcolor.hpp</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Copyright: 2013 Ihor Kalnytskyi</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">License: BSD</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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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Copyright: 2021 Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">License: LGPL-3.0+</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">License: LGPL-3.0+</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> This package is free software; you can redistribute it and/or</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> modify it under the terms of the GNU Lesser General Public</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> License as published by the Free Software Foundation; either</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> version 3 of the License, or (at your option) any later version.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> This package is distributed in the hope that it will be useful,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> Lesser General Public License for more details.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> You should have received a copy of the GNU Lesser General Public License</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> along with this program. If not, see <https://www.gnu.org/licenses/>.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> On Debian systems, the complete text of the GNU Lesser General</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> Public License can be found in "/usr/share/common-licenses/LGPL-3".</span></pre>
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<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#7ef1b627993b64c5dae251ea3c9df445df15d006"><strong>debian/libcmdock0.install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#f871d7525a5d14815942d2eaa525f7174af6d238"><strong>debian/patches/installdir.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller <moeller@debian.org></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Adjusting install paths to mostly fit Debian policy</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarding: Not required.</span></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">Index: cmdock-0.1.3/meson.build</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/meson.build</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/meson.build</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -109,7 +109,7 @@</span> libcmdock = library(</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> version : meson.project_version(),</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> include_directories : incRbt, </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> install : true,</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install_dir: './build'</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ install_dir: './lib'</span></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>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> cxxopts_dep = dependency('cxxopts', fallback : ['cxxopts', 'cxxopts_dep'])</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -118,42 +118,42 @@</span> cmdock = executable(</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> 'cmdock', 'src/exe/cmdock.cxx', link_with : libcmdock,</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> dependencies : [cxxopts_dep, eigen3_dep, pcg_cpp_dep],</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> include_directories : incRbt, install : true,</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install_dir: './build'</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ install_dir: './bin'</span></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"> cmcavity = executable(</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> 'cmcavity', 'src/exe/cmcavity.cxx', link_with : libcmdock,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> dependencies : [cxxopts_dep, eigen3_dep, pcg_cpp_dep],</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> include_directories : incRbt, install : true,</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install_dir: './build'</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ install_dir: './bin'</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> executable(</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> 'cmrms', 'src/exe/cmrms.cxx', link_with : libcmdock,</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> dependencies : eigen3_dep,</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> include_directories : incRbt, install: true,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install_dir: './build'</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ install_dir: './bin'</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> executable(</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> 'cmmoegrid', 'src/exe/cmmoegrid.cxx', link_with : libcmdock,</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> dependencies : [cxxopts_dep, eigen3_dep, pcg_cpp_dep],</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> include_directories : incRbt, install : true,</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install_dir: './build'</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ install_dir: './bin'</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> executable(</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> 'cmlist', 'src/exe/cmlist.cxx', link_with : libcmdock,</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> dependencies : eigen3_dep,</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> include_directories : incRbt, install : true,</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install_dir: './build'</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ install_dir: './bin'</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> )</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> executable(</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> 'cmcalcgrid', 'src/exe/cmcalcgrid.cxx', link_with : libcmdock,</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> dependencies : [eigen3_dep, pcg_cpp_dep], include_directories : incRbt,</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> install : true,</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install_dir: './build'</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ install_dir: './bin'</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> executable(</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> 'cmconvgrid', 'src/exe/cmconvgrid.cxx', link_with : libcmdock,</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> dependencies : eigen3_dep, include_directories : incRbt, install : true,</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install_dir: './build'</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ install_dir: './bin'</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> dt_smarts_dep = dependency('dt_smarts', required : false)</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">@@ -178,11 +178,11 @@</span> endif</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> # Copy entire folder with subfolders</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> # Scripts in bin</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-install_subdir('bin', install_dir : './')</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+install_subdir('bin', install_dir : '.')</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> # Data and protocols</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-install_subdir('data', install_dir : './')</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+install_subdir('data', install_dir : './share/cmdock/')</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> # Perl scripts</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;">-install_subdir('lib', install_dir : './')</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;">+install_subdir('lib', install_dir : './share/cmdock/')</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> tests_opt = get_option('tests')</span></pre>
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<li id="be445773d38b48f6f98e814a57b89a3e7151bcef">
<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#be445773d38b48f6f98e814a57b89a3e7151bcef"><strong>debian/patches/noPCGtest.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Hack to overcome difficulty to spot pcg library</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarding: Not required.</span></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">Index: cmdock-0.1.3/meson.build</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/meson.build</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/meson.build</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -93,12 +93,13 @@</span> endif</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> # Use standard C++11 RNG on Solaris and Windows/MSVC due to PCG build failure</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> # Solaris issue: https://github.com/imneme/pcg-cpp/issues/42</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> # Windows/MSVC issue: https://github.com/imneme/pcg-cpp/issues/11</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if (host_machine.system() == 'sunos' or (host_machine.system() == 'windows' and</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cpp_compiler.get_id() == 'msvc'))</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pcg_cpp_dep = declare_dependency()</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pcg_cpp_dep = dependency('pcg-cpp', fallback : ['pcg', 'pcg_cpp_dep'])</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if (host_machine.system() == 'sunos' or (host_machine.system() == 'windows' and</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# cpp_compiler.get_id() == 'msvc'))</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;">+# pcg_cpp_dep = declare_dependency()</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# pcg_cpp_dep = dependency('pcg-cpp', fallback : ['pcg', 'pcg_cpp_dep'])</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+pcg_cpp_dep = dependency('pcg', required : false)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> library_soversion = meson.project_version().split('.')[0]</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> libcmdock = library(</span></pre>
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<li id="75530a216b34342639a71cc6c2be7fdc37b3d77b">
<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#75530a216b34342639a71cc6c2be7fdc37b3d77b"><strong>debian/patches/pythonVersion.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller <moeller@debian.org></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Adjusting paths of interpreters.</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarding: Not required.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Index: cmdock-0.1.3/bin/rbhtfinder</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/bin/rbhtfinder</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/bin/rbhtfinder</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl -w</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl -w</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> # Script that simulates the result of a high throughput protocol.</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: cmdock-0.1.3/bin/run_rbdock.pl</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/bin/run_rbdock.pl</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/bin/run_rbdock.pl</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> use lib "$ENV{'CMDOCK_ROOT'}/lib";</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> require "run_rbfuncs.pl";</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: cmdock-0.1.3/bin/run_rbscreen.pl</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/bin/run_rbscreen.pl</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/bin/run_rbscreen.pl</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> use File::stat;</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> use lib "$ENV{'CMDOCK_ROOT'}/lib";</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> use strict;</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: cmdock-0.1.3/bin/sdfield</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/bin/sdfield</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/bin/sdfield</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> # add extra fields to SD records</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> use lib "$ENV{'CMDOCK_ROOT'}/lib";</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> use SDRecord;</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: cmdock-0.1.3/bin/sdfilter</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/bin/sdfilter</span></span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/bin/sdfilter</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> # Filters SD records by given data field *</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"> # Usage: sdfilter -f'$<DataField> <Operator> <Value>' [sdFiles] *</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: cmdock-0.1.3/bin/sdmodify</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/bin/sdmodify</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/bin/sdmodify</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> # Script to set the first title line equal to a given data field</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> # Usage: sdmodify -f<DataField> [sdFiles]</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: cmdock-0.1.3/bin/sdreport</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/bin/sdreport</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/bin/sdreport</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> # Produces text summaries of SD records *</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> # *</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> # Usage: sdreport [-l] [-t] [-s<DataField>] [sdFiles] *</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: cmdock-0.1.3/bin/sdrmsd</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/bin/sdrmsd</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/bin/sdrmsd</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#! /usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> # Calculate SMART RMSD with or without molecular superposition (FIT or NOFIT) </span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> # Script distributed under GNU LGPL 3.0 along rDock software.</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: cmdock-0.1.3/bin/sdsort</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/bin/sdsort</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/bin/sdsort</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> # Sorts SD records by given data field</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> use lib "$ENV{'CMDOCK_ROOT'}/lib";</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: cmdock-0.1.3/bin/sdsplit</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/bin/sdsplit</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/bin/sdsplit</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> # Splits SD records into multiple files of equal no. of records</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> use lib "$ENV{'CMDOCK_ROOT'}/lib";</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> </span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: cmdock-0.1.3/data/pmf/smoothed/m2pmf.awk</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/data/pmf/smoothed/m2pmf.awk</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/data/pmf/smoothed/m2pmf.awk</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/awk -f</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/awk -f</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> BEGIN{</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> true = 1;</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> false = !true;</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: cmdock-0.1.3/data/pmf/smoothed/pmf2m.awk</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/data/pmf/smoothed/pmf2m.awk</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/data/pmf/smoothed/pmf2m.awk</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/awk -f</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/awk -f</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> {</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> a[NR]=$1;</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> b[NR]=$2;</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: cmdock-0.1.3/bin/sdtether</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cmdock-0.1.3.orig/bin/sdtether</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cmdock-0.1.3/bin/sdtether</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#! /usr/bin/env python</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#! /usr/bin/python3</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> #</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> # Substitute for rbtether of rDock. Will align input molecules to a reference fragment defined by a smarts string, </span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> # it will add a TETHERED ATOM property field to the output SDF that is correctly understood by rDock </span></pre>
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<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">noPCGtest.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">installdir.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">pythonVersion.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">export DH_VERBOSE = 1</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">#export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">%:</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> dh $@</span></pre>
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<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># For more information on what jobs are run see:</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># https://salsa.debian.org/salsa-ci-team/pipeline</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># To enable the jobs, go to your repository (at salsa.debian.org)</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># and click over Settings > CI/CD > Expand (in General pipelines).</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># In "Custom CI config path" write debian/salsa-ci.yml and click</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># in "Save Changes". The CI tests will run after the next commit.</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0 (quilt)</span></pre>
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<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">---</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">References:</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> - Author: Jukič, M., Škrlj, B., Tomšič, G., Pleško, S., Podlipnik Č., Bren, U.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Year: 2021</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Prioritisation of Compounds for 3CLpro Inhibitor Development on SARS-CoV-2 Variants.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Journal: Molecules</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Volume: 26</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Numer: 10</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Pages: 3003</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> DOI: 10.3390/molecules26103003</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> URL: https://www.mdpi.com/1420-3049/26/10/3003</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> - Author: Ruiz-Carmona, S., Alvarez-Garcia, D., Foloppe, N. Garmendia-Doval, A. B., Juhos S., et al.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Year: 2014</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Journal: PLoS Comput Biol</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> Volume: 10</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Number: 4</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Pages: e1003571</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> DOI: 10.1371/journal.pcbi.1003571</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> Volume: https://doi.org/10.1371/journal.pcbi.1003571</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> - Author: Morley, S. D. and Afshar, M.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> Year: 2004</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> Title: Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> Journal: J. Comput. Aided. Mol. Des.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> Volume: 18</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> Pages: 189-208</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> DOI: 10.1023/B:JCAM.0000035199.48747.1e</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> URL: https://doi.org/10.1023/B:JCAM.0000035199.48747.1e</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> - Name: bio.tools</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> Entry: NA</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> Checked: 2021-06-06</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> Entry: NA</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> Checked: 2021-06-06</span></pre>
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<a href="https://salsa.debian.org/med-team/cmdock/-/commit/e298446b2c652c41923773b7a125a825aa864256#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.bz2%cmdock-$1.tar.bz2%" \</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> https://gitlab.com/Jukic/cmdock/-/releases \</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> (?:.*?/)?cmdock-v(\d[\d.]*)\.tar\.bz2</span></pre>
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