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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/259437d3ee7671dac78fe2141090566048e47d46">259437d3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-28T15:12:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move database to var to enable users recreation of the database
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prokka/commit/a97fba2f8bb68dd2fa82991c21fc7588fa992425">a97fba2f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-28T15:12:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Symlinks to data files on /var/lib to /usr/share
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prokka/commit/5867f5705d8effd15c588f3ffd55909cac944f04">5867f570</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-28T15:16:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleanup on purge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prokka/commit/fa66f09bdb689351a2b6d7887203ac289ab4503d">fa66f09b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-28T15:32:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make db dir user writable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/prokka/commit/1b3ad84c682b9b2af283613be8a1c9d1fb1f7b32">1b3ad84c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-28T17:22:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix permissions
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
<span class="deleted-file">
−
debian/README.Debian
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#c7d317ff5f67a0d69bdebe0b1fad72b2750a6dda">
debian/patches/set-db-dir
</a>
</li>
<li class="file-stats">
<a href="#a7bbea1fca7c7cd4f5589fab806bd8bd9166767e">
debian/prokka.postinstall
→
debian/prokka.postinst
</a>
</li>
<li class="file-stats">
<a href="#aac112ef92be3489dfd7e6b3c195671ae7f4cce5">
<span class="new-file">
+
debian/prokka.postrm
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/prokka/compare/a04766af36e117512eff77c0bfd604d84acbe0c8...1b3ad84c682b9b2af283613be8a1c9d1fb1f7b32#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong>
deleted
</a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Prokka's databases are installed to /usr/share/prokka</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">HAMAP.hmm is 224M, took 21 hours and 10 minutes, 15M of memory, single threaded?</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Shipped HAMAP.hmm is 88M ??</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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<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">After installing the package you need to run</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"> prokka --setupdb</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="LC12" class="line" lang="plaintext">as root. This is creates files</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> /usr/share/prokka/db/kingdom/Archaea/sprot.{phr,pin,psq}</span>
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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">which is not policy compliant. It would be better to move the db to</span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> /var/lib/prokka/db</span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">instead.</span></pre>
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<a href="https://salsa.debian.org/med-team/prokka/compare/a04766af36e117512eff77c0bfd604d84acbe0c8...1b3ad84c682b9b2af283613be8a1c9d1fb1f7b32#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -2,6 +2,5 @@ prokka (1.13.4+dfsg-1) UNRELEASED; urgency=low</td>
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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="LC4" class="line" lang="plaintext"> * Initial release (Closes: #778246)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> TODO: See README.Debian about user generated files in /usr</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 28 Jan 2019 13:26:30 +0100</span></pre>
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<a href="https://salsa.debian.org/med-team/prokka/compare/a04766af36e117512eff77c0bfd604d84acbe0c8...1b3ad84c682b9b2af283613be8a1c9d1fb1f7b32#c7d317ff5f67a0d69bdebe0b1fad72b2750a6dda"><strong>debian/patches/set-db-dir</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">@@ -13,7 +13,7 @@ Last-Update: 2015-02-21</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> # where to put formatted database: /path/to/prokka/db/</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;">-ROOTDIR=$(dirname $0)</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ROOTDIR=/<span class="idiff left right">usr/share</span>/prokka/db</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ROOTDIR=/<span class="idiff left right">var/lib</span>/prokka/db</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> echo "*** NOTICE ***"</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> echo "This script is about to download data from the Internet and overwrite your existing Prokka BLAST databases."</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">@@ -33,7 +33,7 @@ Last-Update: 2015-02-21</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> $metagenome, $compliant, $listdb, $citation);</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$dbdir = $ENV{'PROKKA_DBDIR'} || abs_path("$FindBin::RealBin/../db");</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$dbdir = "/<span class="idiff left right">usr/share</span>/prokka/db";</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$dbdir = "/<span class="idiff left right">var/lib</span>/prokka/db";</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> setOptions();</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> </span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,6 +17,7 @@ set -e</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># for details, see http://www.debian.org/doc/debian-policy/ or</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># the debian-policy package</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#PROKKADBPATH=/var/lib/prokka/db</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">case</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>configure<span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/prokka/compare/a04766af36e117512eff77c0bfd604d84acbe0c8...1b3ad84c682b9b2af283613be8a1c9d1fb1f7b32#aac112ef92be3489dfd7e6b3c195671ae7f4cce5"><strong>debian/prokka.postrm</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</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="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-e</span> </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="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="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"purge"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-d</span> <span class="nv" style="color: teal;">$PROKKADBPATH</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: teal;">$PROKKADBPATH</span><span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="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="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#DEBHELPER# </span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/prokka/compare/a04766af36e117512eff77c0bfd604d84acbe0c8...1b3ad84c682b9b2af283613be8a1c9d1fb1f7b32#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">@@ -2,6 +2,10 @@</td>
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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">DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">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/db</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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></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">@@ -10,3 +14,17 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">override_dh_link:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> for db in `find debian/$(DEB_SOURCE)/usr/share/prokka/db -type f` ; do \</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> vardir=`echo $${db} | sed -e 's?.*/usr/share?/var/lib?'` ; \</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> mkdir -p debian/$(DEB_SOURCE)/`dirname $${vardir}` ; \</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> usrdir=`echo $${db} | sed -e 's?.*/usr?/usr?'` ; \</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> dh_link $${usrdir} $${vardir} ; \</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> done</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">override_dh_fixperms:</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> dh_fixperms</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> for db in `find debian/$(DEB_SOURCE)/$(PROKKADBPATH) -type d` ; do \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> chmod a+w $${db} ; \</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> done</span></pre>
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