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<h3>
Saira Hussain pushed to branch master
at <a href="https://salsa.debian.org/med-team/hisat2">Debian Med / hisat2</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/commit/74e387eebc507dea7f3b68bdf15c65390ef43e43">74e387ee</a></strong>
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<span>by Saira Hussain</span>
<i>at 2019-08-02T14:17:42Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests template
</pre>
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<strong><a href="https://salsa.debian.org/med-team/hisat2/commit/58054b964da0e3eaa538934537760fab4bc5e305">58054b96</a></strong>
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<span>by Saira Hussain</span>
<i>at 2019-08-02T14:18:40Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump changelog
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<h4>4 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#f460019ffb3c4e7d7f10863146c3e4d07f471ed5">
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debian/example
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<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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debian/tests/control
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<li class="file-stats">
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debian/tests/run-unit-tests
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/hisat2/compare/8c33f70533310cf602c9028e42994a262987a36a...58054b964da0e3eaa538934537760fab4bc5e305#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hisat2 (2.1.0-4) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</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"> [Saira Hussain]</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Add autopkgtest</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"> -- Saira Hussain <saira.h0213@zoho.com> Fri, 02 Aug 2019 15:18:09 +0100</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">hisat2 (2.1.0-3) UNRELEASED; urgency=medium</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"> * Install hisat2_extract_splice_sites.py</span>
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<li id="f460019ffb3c4e7d7f10863146c3e4d07f471ed5">
<a href="https://salsa.debian.org/med-team/hisat2/compare/8c33f70533310cf602c9028e42994a262987a36a...58054b964da0e3eaa538934537760fab4bc5e305#f460019ffb3c4e7d7f10863146c3e4d07f471ed5"><strong>debian/example</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">example/*</span></pre>
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<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/hisat2/compare/8c33f70533310cf602c9028e42994a262987a36a...58054b964da0e3eaa538934537760fab4bc5e305#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-tests</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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<li id="b8880ead45e8d099a1552defb95ea70479f1572e">
<a href="https://salsa.debian.org/med-team/hisat2/compare/8c33f70533310cf602c9028e42994a262987a36a...58054b964da0e3eaa538934537760fab4bc5e305#b8880ead45e8d099a1552defb95ea70479f1572e"><strong>debian/tests/run-unit-tests</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/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>hisat2</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" 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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</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>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Just for debugging</span></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;">set</span> <span class="nt" style="color: #000080;">-x</span></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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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run the reproducible suite</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span></pre>
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