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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bali-phy">Debian Med / bali-phy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bali-phy/commit/ff28db02a69cfe2c74575a63db96637c06f4ec31">ff28db02</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-11T07:46:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move single test scripts into single script and fix the new location of examples
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bali-phy/commit/eb4c937ca4b5370f439f2917db6c44bddd1d68c8">eb4c937c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-11T07:47:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install autopkgtest script into usr/share/doc to enable users reproducing the tests on their local machine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bali-phy/commit/b0663953b8e91d84fd191ab98908528932b1a1ea">b0663953</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-11T07:51:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Users are not permitted to write to /usr/share/doc - move examples to temporary dir to let the script work under all circumstances
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bali-phy/commit/c7ca5c91ecb55344e15ebece3a8fba806be6f23f">c7ca5c91</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-11T08:15:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
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<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
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+
debian/docs
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#d4b96b44b35b082a21400aad5c580c5269de9053">
<span class="deleted-file">
−
debian/tests/help
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
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+
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#7bc147a853f3acf96854d25092a18a903eab754d">
<span class="deleted-file">
−
debian/tests/small-A
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<li class="file-stats">
<a href="#ec41940a4249250fd849d92e9fec60b076b5a28b">
<span class="deleted-file">
−
debian/tests/small-analysis
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<li class="file-stats">
<a href="#8519c8d8a49bc8136b28a8f1a39f786ee343a59a">
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debian/tests/small-no-A
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<li class="file-stats">
<a href="#38812982c0bd7bb66f541124625baeb4ad121d20">
<span class="deleted-file">
−
debian/tests/small-test
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<li class="file-stats">
<a href="#b95cf236adf378c932f18117199baf08b744d911">
<span class="deleted-file">
−
debian/tests/version
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</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="k" style="font-weight: 600;">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">executing</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">bali-phy (3.0.2+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">bali-phy (3.0.2+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: #891971).</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"> -- Benjamin Redelings <benjamin.redelings@gmail.com> <span class="idiff left right">Tue, 06 Mar 2018 22:01:35 -05</span>00</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Benjamin Redelings <benjamin.redelings@gmail.com> <span class="idiff left right">Sun, 11 Mar 2018 07:28:17 +01</span>00</span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Tests: version, help, small-test, small-A, small-no-A, small-analysis</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f#d4b96b44b35b082a21400aad5c580c5269de9053"><strong>debian/tests/help</strong>
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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">bali-phy <span class="nt" style="color: navy;">--help</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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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4
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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;">pkg</span><span class="o" style="font-weight: 600;">=</span>bali-phy</span>
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6
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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 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;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>mktemp <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell">cp <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">bali-phy <span class="nt" style="color: navy;">--version</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">bali-phy <span class="nt" style="color: navy;">--help</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">bali-phy sequences/5S-rRNA/5d.fasta <span class="nt" style="color: navy;">--test</span> <span class="nt" style="color: navy;">--seed</span><span class="o" style="font-weight: 600;">=</span>0</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">bali-phy sequences/5S-rRNA/5d.fasta <span class="nt" style="color: navy;">--iter</span><span class="o" style="font-weight: 600;">=</span>50 <span class="nt" style="color: navy;">--seed</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">bali-phy sequences/5S-rRNA/5d.fasta <span class="nt" style="color: navy;">--iter</span><span class="o" style="font-weight: 600;">=</span>200 <span class="nt" style="color: navy;">-Inone</span> <span class="nt" style="color: navy;">--seed</span><span class="o" style="font-weight: 600;">=</span>0</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">bali-phy sequences/5S-rRNA/5d.fasta <span class="nt" style="color: navy;">--iter</span><span class="o" style="font-weight: 600;">=</span>100</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">bp-analyze 5d-1</span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f#7bc147a853f3acf96854d25092a18a903eab754d"><strong>debian/tests/small-A</strong>
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1
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell">bali-phy /usr/share/bali-phy/examples/sequences/5S-rRNA/5d.fasta <span class="nt" style="color: navy;">--iter</span><span class="o" style="font-weight: 600;">=</span>50 <span class="nt" style="color: navy;">--seed</span><span class="o" style="font-weight: 600;">=</span>0</span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f#ec41940a4249250fd849d92e9fec60b076b5a28b"><strong>debian/tests/small-analysis</strong>
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell">bali-phy /usr/share/bali-phy/examples/sequences/5S-rRNA/5d.fasta <span class="nt" style="color: navy;">--iter</span><span class="o" style="font-weight: 600;">=</span>100</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell">bp-analyze 5d-1</span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f#8519c8d8a49bc8136b28a8f1a39f786ee343a59a"><strong>debian/tests/small-no-A</strong>
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1
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell">bali-phy /usr/share/bali-phy/examples/sequences/5S-rRNA/5d.fasta <span class="nt" style="color: navy;">--iter</span><span class="o" style="font-weight: 600;">=</span>200 <span class="nt" style="color: navy;">-Inone</span> <span class="nt" style="color: navy;">--seed</span><span class="o" style="font-weight: 600;">=</span>0</span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f#38812982c0bd7bb66f541124625baeb4ad121d20"><strong>debian/tests/small-test</strong>
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell">bali-phy /usr/share/bali-phy/examples/sequences/5S-rRNA/5d.fasta <span class="nt" style="color: navy;">--test</span> <span class="nt" style="color: navy;">--seed</span><span class="o" style="font-weight: 600;">=</span>0</span></pre>
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<a href="https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f#b95cf236adf378c932f18117199baf08b744d911"><strong>debian/tests/version</strong>
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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">bali-phy <span class="nt" style="color: navy;">--version</span></span></pre>
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