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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/prokka">Debian Med / prokka</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/prokka/commit/0b187b65e449d4c89cf6b85a0bf6ae069737e8d4">0b187b65</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-02-04T08:19:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Exclude non-free data files and provide script to fetch and install these if needed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prokka/commit/daf27376471d1abaf5406da7f849d07f6323a591">daf27376</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-02-04T08:19:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.13.4+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prokka/commit/b7a394b3110fc414e2fb8db8af27ac6a9b85534f">b7a394b3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-02-04T08:20:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.13.4+dfsg'
Update to upstream version '1.13.4+dfsg'
with Debian dir 2f98d1ead36636e4362f05cd2af41403297cb7c4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prokka/commit/5355136ab1950644b9bf9e2200bd3466689a574f">5355136a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-02-04T08:59:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix permissions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prokka/commit/7e2ab564367f45645df64231269d27b30abb8861">7e2ab564</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-02-04T09:05:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#15a3036fe7b3364b4df17b8dd76a41eceae9b6aa">
<span class="deleted-file">
−
db/hmm/HAMAP.hmm
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<li class="file-stats">
<a href="#183559170bba0c13943404c29ced00eff02e1175">
<span class="deleted-file">
−
db/kingdom/Archaea/sprot
</span>
</a>
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<li class="file-stats">
<a href="#a86e8e984fc1c033c55242b0d1c2778631a60527">
<span class="deleted-file">
−
db/kingdom/Bacteria/AMR
</span>
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<li class="file-stats">
<a href="#dbb95dc45b1321f6b66bfdad83554cbbf890b037">
<span class="deleted-file">
−
db/kingdom/Bacteria/IS
</span>
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<li class="file-stats">
<a href="#bb3f2d3668cb7051b5f618c3540217a32c4bbbc4">
<span class="deleted-file">
−
db/kingdom/Bacteria/sprot
</span>
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<a href="#a7a2350e06392acc1758e465e53b2362c1cbb07a">
<span class="deleted-file">
−
db/kingdom/Mitochondria/sprot
</span>
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<li class="file-stats">
<a href="#e5626c25bfa779f8e06e03559a6ae8952dcaa2a9">
<span class="deleted-file">
−
db/kingdom/Viruses/sprot
</span>
</a>
</li>
<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
<span class="new-file">
+
debian/README.Debian
</span>
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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<li class="file-stats">
<a href="#916eb8b106a13f92f5f826ae5fa014531c257426">
<span class="new-file">
+
debian/get-additional-data
</span>
</a>
</li>
<li class="file-stats">
<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
debian/lintian-overrides
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="15a3036fe7b3364b4df17b8dd76a41eceae9b6aa">
<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#15a3036fe7b3364b4df17b8dd76a41eceae9b6aa"><strong>db/hmm/HAMAP.hmm</strong>
deleted
</a>
<hr>
No preview for this file type
<br>
</li>
<li id="183559170bba0c13943404c29ced00eff02e1175">
<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#183559170bba0c13943404c29ced00eff02e1175"><strong>db/kingdom/Archaea/sprot</strong>
deleted
</a>
The diff for this file was not included because it is too large.
<br>
</li>
<li id="a86e8e984fc1c033c55242b0d1c2778631a60527">
<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#a86e8e984fc1c033c55242b0d1c2778631a60527"><strong>db/kingdom/Bacteria/AMR</strong>
deleted
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The diff for this file was not included because it is too large.
<br>
</li>
<li id="dbb95dc45b1321f6b66bfdad83554cbbf890b037">
<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#dbb95dc45b1321f6b66bfdad83554cbbf890b037"><strong>db/kingdom/Bacteria/IS</strong>
deleted
</a>
The diff for this file was not included because it is too large.
<br>
</li>
<li id="bb3f2d3668cb7051b5f618c3540217a32c4bbbc4">
<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#bb3f2d3668cb7051b5f618c3540217a32c4bbbc4"><strong>db/kingdom/Bacteria/sprot</strong>
deleted
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The diff for this file was not included because it is too large.
<br>
</li>
<li id="a7a2350e06392acc1758e465e53b2362c1cbb07a">
<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#a7a2350e06392acc1758e465e53b2362c1cbb07a"><strong>db/kingdom/Mitochondria/sprot</strong>
deleted
</a>
The diff for this file was not included because it is too large.
<br>
</li>
<li id="e5626c25bfa779f8e06e03559a6ae8952dcaa2a9">
<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#e5626c25bfa779f8e06e03559a6ae8952dcaa2a9"><strong>db/kingdom/Viruses/sprot</strong>
deleted
</a>
The diff for this file was not included because it is too large.
<br>
</li>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">prokka for Debian</span>
</pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">=================</span>
</pre>
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3
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Some data files of prokka are licensed CC-BY-ND-3 which is considered</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">non-free by Debian. These files are excluded from the distributed</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">source. You can obtain these files by calling</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> sh /usr/share/doc/prokka/get-additional-data</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 28 Jan 2019 18:52:07 +0100</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">prokka (1.13.4+dfsg-1) unstable; urgency=low</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"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #778246)</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, <span class="idiff left right">28 Jan 2019 18:52:07</span> +0100</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, <span class="idiff left right">04 Feb 2019 10:00:06</span> +0100</span></pre>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#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">@@ -2,28 +2,13 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: Prokka</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: https://github.com/tseemann/prokka/releases</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Files-Excluded: binaries/*</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> db/hmm</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> db/kingdom</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Copyright: Copyright (C) 2012-2018 Torsten Seemann</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">License: GPL-3+</span>
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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="LC10" class="line" lang="plaintext">Files: db/hmm/*</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> db/kingdom/*</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Copyright: UniProtKB/Swiss-Prot is copyrighted by the UniProt Consortium</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">License: CC-BY-ND-3</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Comment: Email from upstream author:</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> From: Torsten Seemann <torsten.seemann@monash.edu></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> Date: Sat, 14 Feb 2015 14:45:55 +1100</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> Message-ID: <CAFrpSegC=noX+M-i-QXJvde-pECpy4uCPP8PQy5qHgHbu3PjaQ@mail.gmail.com></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> Subject: Re: Prokka Debian package?</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> To: "Michael R. Crusoe" <mcrusoe@msu.edu></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"> > ./db/kingdom/Archaea/sprot</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> > ./db/kingdom/Bacteria/sprot</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> > ./db/kingdom/Mitochondria/sprot</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> > ./db/kingdom/Viruses/sprot</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> These 3 are derived from UniProt.</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Files: db/cm/*</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Copyright: Wellcome Trust Sanger Institute</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">License: CC0-1</span>
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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">@@ -34,58 +19,6 @@ Copyright: 2015 Michael R. Crusoe <mcrusoe@msu.edu></td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> 2016-2019 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">License: GPL-3+</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="LC37" class="line" lang="plaintext">License: CC-BY-ND-3</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS OF THIS CREATIVE COMMONS PUBLIC LICENSE ("CCPL" OR "LICENSE"). THE WORK IS PROTECTED BY COPYRIGHT AND/OR OTHER APPLICABLE LAW. ANY USE OF THE WORK OTHER THAN AS AUTHORIZED UNDER THIS LICENSE OR COPYRIGHT LAW IS PROHIBITED.</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> 1. Definitions</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> "Adaptation" means a work based upon the Work, or upon the Work and other pre-existing works, such as a translation, adaptation, derivative work, arrangement of music or other alterations of a literary or artistic work, or phonogram or performance and includes cinematographic adaptations or any other form in which the Work may be recast, transformed, or adapted including in any form recognizably derived from the original, except that a work that constitutes a Collection will not be considered an Adaptation for the purpose of this License. For the avoidance of doubt, where the Work is a musical work, performance or phonogram, the synchronization of the Work in timed-relation with a moving image ("synching") will be considered an Adaptation for the purpose of this License.</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> "Distribute" means to make available to the public the original and copies of the Work through sale or other transfer of ownership.</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> "Licensor" means the individual, individuals, entity or entities that offer(s) the Work under the terms of this License.</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> "Original Author" means, in the case of a literary or artistic work, the individual, individuals, entity or entities who created the Work or if no individual or entity can be identified, the publisher; and in addition (i) in the case of a performance the actors, singers, musicians, dancers, and other persons who act, sing, deliver, declaim, play in, interpret or otherwise perform literary or artistic works or expressions of folklore; (ii) in the case of a phonogram the producer being the person or legal entity who first fixes the sounds of a performance or other sounds; and, (iii) in the case of broadcasts, the organization that transmits the broadcast.</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> "Work" means the literary and/or artistic work offered under the terms of this License including without limitation any production in the literary, scientific and artistic domain, whatever may be the mode or form of its expression including digital form, such as a book, pamphlet and other writing; a lecture, address, sermon or other work of the same nature; a dramatic or dramatico-musical work; a choreographic work or entertainment in dumb show; a musical composition with or without words; a cinematographic work to which are assimilated works expressed by a process analogous to cinematography; a work of drawing, painting, architecture, sculpture, engraving or lithography; a photographic work to which are assimilated works expressed by a process analogous to photography; a work of applied art; an illustration, map, plan, sketch or three-dimensional work relative to geography, topography, architecture or science; a performance; a broadcast; a phonogram; a compilation of data to the extent it is protected as a copyrightable work; or a work performed by a variety or circus performer to the extent it is not otherwise considered a literary or artistic work.</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> "You" means an individual or entity exercising rights under this License who has not previously violated the terms of this License with respect to the Work, or who has received express permission from the Licensor to exercise rights under this License despite a previous violation.</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> "Publicly Perform" means to perform public recitations of the Work and to communicate to the public those public recitations, by any means or process, including by wire or wireless means or public digital performances; to make available to the public Works in such a way that members of the public may access these Works from a place and at a place individually chosen by them; to perform the Work to the public by any means or process and the communication to the public of the performances of the Work, including by public digital performance; to broadcast and rebroadcast the Work by any means including signs, sounds or images.</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> "Reproduce" means to make copies of the Work by any means including without limitation by sound or visual recordings and the right of fixation and reproducing fixations of the Work, including storage of a protected performance or phonogram in digital form or other electronic medium.</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> 2. Fair Dealing Rights. Nothing in this License is intended to reduce, limit, or restrict any uses free from copyright or rights arising from limitations or exceptions that are provided for in connection with the copyright protection under copyright law or other applicable laws.</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> 3. License Grant. Subject to the terms and conditions of this License, Licensor hereby grants You a worldwide, royalty-free, non-exclusive, perpetual (for the duration of the applicable copyright) license to exercise the rights in the Work as stated below:</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> to Reproduce the Work, to incorporate the Work into one or more Collections, and to Reproduce the Work as incorporated in the Collections; and,</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> to Distribute and Publicly Perform the Work including as incorporated in Collections.</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> For the avoidance of doubt:</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> Non-waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing scheme cannot be waived, the Licensor reserves the exclusive right to collect such royalties for any exercise by You of the rights granted under this License;</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> Waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing scheme can be waived, the Licensor waives the exclusive right to collect such royalties for any exercise by You of the rights granted under this License; and,</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> Voluntary License Schemes. The Licensor waives the right to collect royalties, whether individually or, in the event that the Licensor is a member of a collecting society that administers voluntary licensing schemes, via that society, from any exercise by You of the rights granted under this License.</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> The above rights may be exercised in all media and formats whether now known or hereafter devised. The above rights include the right to make such modifications as are technically necessary to exercise the rights in other media and formats, but otherwise you have no rights to make Adaptations. Subject to Section 8(f), all rights not expressly granted by Licensor are hereby reserved.</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> 4. Restrictions. The license granted in Section 3 above is expressly made subject to and limited by the following restrictions:</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> You may Distribute or Publicly Perform the Work only under the terms of this License. You must include a copy of, or the Uniform Resource Identifier (URI) for, this License with every copy of the Work You Distribute or Publicly Perform. You may not offer or impose any terms on the Work that restrict the terms of this License or the ability of the recipient of the Work to exercise the rights granted to that recipient under the terms of the License. You may not sublicense the Work. You must keep intact all notices that refer to this License and to the disclaimer of warranties with every copy of the Work You Distribute or Publicly Perform. When You Distribute or Publicly Perform the Work, You may not impose any effective technological measures on the Work that restrict the ability of a recipient of the Work from You to exercise the rights granted to that recipient under the terms of the License. This Section 4(a) applies to the Work as incorporated in a Collection, but this does not require the Collection apart from the Work itself to be made subject to the terms of this License. If You create a Collection, upon notice from any Licensor You must, to the extent practicable, remove from the Collection any credit as required by Section 4(b), as requested.</span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> If You Distribute, or Publicly Perform the Work or Collections, You must, unless a request has been made pursuant to Section 4(a), keep intact all copyright notices for the Work and provide, reasonable to the medium or means You are utilizing: (i) the name of the Original Author (or pseudonym, if applicable) if supplied, and/or if the Original Author and/or Licensor designate another party or parties (e.g., a sponsor institute, publishing entity, journal) for attribution ("Attribution Parties") in Licensor's copyright notice, terms of service or by other reasonable means, the name of such party or parties; (ii) the title of the Work if supplied; (iii) to the extent reasonably practicable, the URI, if any, that Licensor specifies to be associated with the Work, unless such URI does not refer to the copyright notice or licensing information for the Work. The credit required by this Section 4(b) may be implemented in any reasonable manner; provided, however, that in the case of a Collection, at a minimum such credit will appear, if a credit for all contributing authors of the Collection appears, then as part of these credits and in a manner at least as prominent as the credits for the other contributing authors. For the avoidance of doubt, You may only use the credit required by this Section for the purpose of attribution in the manner set out above and, by exercising Your rights under this License, You may not implicitly or explicitly assert or imply any connection with, sponsorship or endorsement by the Original Author, Licensor and/or Attribution Parties, as appropriate, of You or Your use of the Work, without the separate, express prior written permission of the Original Author, Licensor and/or Attribution Parties.</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> 5. Representations, Warranties and Disclaimer</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> 6. Limitation on Liability. EXCEPT TO THE EXTENT REQUIRED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE TO YOU ON ANY LEGAL THEORY FOR ANY SPECIAL, INCIDENTAL, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES ARISING OUT OF THIS LICENSE OR THE USE OF THE WORK, EVEN IF LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"> 7. Termination</span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"> This License and the rights granted hereunder will terminate automatically upon any breach by You of the terms of this License. Individuals or entities who have received Collections from You under this License, however, will not have their licenses terminated provided such individuals or entities remain in full compliance with those licenses. Sections 1, 2, 5, 6, 7, and 8 will survive any termination of this License.</span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"> 8. Miscellaneous</span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"> Each time You Distribute or Publicly Perform the Work or a Collection, the Licensor offers to the recipient a license to the Work on the same terms and conditions as the license granted to You under this License.</span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext"> If any provision of this License is invalid or unenforceable under applicable law, it shall not affect the validity or enforceability of the remainder of the terms of this License, and without further action by the parties to this agreement, such provision shall be reformed to the minimum extent necessary to make such provision valid and enforceable.</span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext"></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">License: CC0-1</span>
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90
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> Statement of Purpose</span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.md</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/get-additional-data</span></pre>
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<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#916eb8b106a13f92f5f826ae5fa014531c257426"><strong>debian/get-additional-data</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh -e</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: teal;">PROKKADBPATH</span><span class="o" style="font-weight: 600;">=</span>/var/lib/prokka/db</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if </span>which prokka <span class="o" style="font-weight: 600;">></span>/dev/null <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># PROKKAVERSION=`prokka -v | sed 's/^.*[[:space:]]\+//'`</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Sometimes prokka reports wrong version</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nv" style="color: teal;">PROKKAVERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>apt-cache policy prokka | <span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^ </span><span class="se" style="color: #d14;">\*\*\*</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^ \*\*\* \([.0-9]\+\)[+-].*/\1/'</span><span class="sb" style="color: #d14;">`</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"prokka not installed."</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-x</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell">wget <span class="nt" style="color: navy;">-np</span> <span class="nt" style="color: navy;">-N</span> https://github.com/tseemann/prokka/archive/v<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PROKKAVERSION</span><span class="k" style="font-weight: 600;">}</span>.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>data <span class="k" style="font-weight: 600;">in </span>hmm kingdom <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-xaf</span> v<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PROKKAVERSION</span><span class="k" style="font-weight: 600;">}</span>.tar.gz <span class="nt" style="color: navy;">--no-anchored</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$data</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PROKKADBPATH</span><span class="k" style="font-weight: 600;">}</span>/<span class="nv" style="color: teal;">$data</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mv </span>prokka-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PROKKAVERSION</span><span class="k" style="font-weight: 600;">}</span>/db/<span class="nv" style="color: teal;">$data</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PROKKADBPATH</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">prokka <span class="nt" style="color: navy;">--setupdb</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">find <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PROKKADBPATH</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: navy;">-type</span> f <span class="nt" style="color: navy;">-exec</span> <span class="nb" style="color: #0086b3;">chmod </span>a+wr <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>data <span class="k" style="font-weight: 600;">in </span>hmm kingdom <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>find <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PROKKADBPATH</span><span class="k" style="font-weight: 600;">}</span>/<span class="nv" style="color: teal;">$data</span> <span class="nt" style="color: navy;">-type</span> d <span class="nt" style="color: navy;">-exec</span> <span class="nb" style="color: #0086b3;">chmod </span>a+wrx <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<li id="efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># /var/lib/prokka/db is intentionally writable for users</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">prokka: non-standard-dir-perm var/lib/prokka/<span class="idiff left right">db/</span>*</span></pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">prokka: non-standard-dir-perm var/lib/prokka/*</span></pre>
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<a href="https://salsa.debian.org/med-team/prokka/compare/24a6cc6cef53db1fdd76490d2b961e97aa31fd80...7e2ab564367f45645df64231269d27b30abb8861#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ DH_VERBOSE := 1</td>
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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">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">PROKKADBPATH=/var/lib/prokka<span class="idiff left right">/db</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">PROKKADBPATH=/var/lib/prokka</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh $@</span>
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