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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/atropos">Debian Med / atropos</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/atropos/commit/408e078949bafe8020d75aeaa0fb448c6c9bae2f">408e0789</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-04-12T14:51:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/atropos/commit/5c30dd0d5138158e2243a8733a4047743c48e413">5c30dd0d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-04-12T15:04:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#07a7f22e4e6c207f79b8edfbc802c8203ceb5c63">
<span class="new-file">
+
debian/atropos.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
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<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
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+
debian/manpages
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<h4>Changes:</h4>
<li id="07a7f22e4e6c207f79b8edfbc802c8203ceb5c63">
<a href="https://salsa.debian.org/med-team/atropos/compare/062f39d62f362b8375b708fca0b8d020f27edb4d...5c30dd0d5138158e2243a8733a4047743c48e413#07a7f22e4e6c207f79b8edfbc802c8203ceb5c63"><strong>debian/atropos.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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<td class="diff-line-num new new_line" 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="plaintext">.TH ATROPOS "1" "April 2019" "atropos 1.1.21" "User Commands"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<td class="diff-line-num new new_line" 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">atropos \- NGS read trimming tool that is specific, sensitive, and speedy</span>
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<td class="diff-line-num new new_line" 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">.SH SYNOPSIS</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B atropos</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-\-config <config file>] <command> [options]</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SS commands</span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext">detect:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Detect adapter sequences directly from read sequences. Use this</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">command if you are unsure if your data has adapters, or if you know that it</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">has adapters but you don't know what are the adapter sequences.</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">error:</span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext">Estimate the sequencing error rate. Use this command to help determine</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">the quality of your data, and to decide the value for the max error rate (\fB\-e\fR)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">parameter. Normal error for an Illumina experiment is around 1% or less. We</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">recommend setting \fB\-e\fR to 10x the empirical error rate.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">qc:</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Compute read\-level statistics. The output is identical to running the</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\&'trim' command with '\-\-stats pre'. Use this command to get an idea of the</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">quality of your raw data.</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">trim:</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Trim adapters and low\-quality bases, and perform other NGS</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">preprocessing. This command provides most of Atropos' functionality.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.SS optional arguments</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">show this help message and exit</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-\-config\fR <config file></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">provide options in a config file</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.P</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Use "atropos <command> \fB\-\-help\fR" to see all options for a specific command.</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">See http://atropos.readthedocs.org/ for full documentation.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.SH SEE ALSO</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Atropos is a fork of Cutadapt 1.10 (</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">https://github.com/marcelm/cutadapt/tree/2f3cc0717aa9ff1e0326ea6bcb36b712950d4999)</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">by John Didion, et al., "Atropos: sensitive, specific, and speedy trimming of</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">NGS reads, submitted.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Cutadapt (https://github.com/marcelm/cutadapt) was developed by Marcel Martin,</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">"Cutadapt Removes Adapter Sequences From High\-Throughput Sequencing Reads,"</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">EMBnet Journal, 2011, 17(1):10\-12.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/atropos/compare/062f39d62f362b8375b708fca0b8d020f27edb4d...5c30dd0d5138158e2243a8733a4047743c48e413#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">atropos (1.1.21+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">atropos (1.1.21+dfsg-1) <span class="idiff left right">unstable</span>; 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: #<span class="idiff left right"><bug></span>)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right">926944</span>)</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"> -- Andreas Tille <tille@debian.org> Fri, 12 Apr 2019 1<span class="idiff left right">3:25:32</span> +0200</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 12 Apr 2019 1<span class="idiff left right">7:04:21</span> +0200</span></pre>
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<a href="https://salsa.debian.org/med-team/atropos/compare/062f39d62f362b8375b708fca0b8d020f27edb4d...5c30dd0d5138158e2243a8733a4047743c48e413#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</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 class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</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: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/atropos/compare/062f39d62f362b8375b708fca0b8d020f27edb4d...5c30dd0d5138158e2243a8733a4047743c48e413#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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