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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/hisat2">Debian Med / hisat2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/commit/cc6402c1d1719fbb727f4e4e3f501998bb25d22f">cc6402c1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T09:25:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/commit/26e6b5d0d1ff0acc64ac1205bd0fc19a23195ca4">26e6b5d0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T09:25:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/commit/77a04d87d58073b1d5252db08d65d045a18b8d51">77a04d87</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T09:25:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/commit/d0fb9f40c31ae45cb68d3a77e2c7cd624d4a0e9f">d0fb9f40</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T09:43:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix wrong path for Perl interpreter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/commit/86b50013e0ba81d7cb8b6bdde3026394e46d18f4">86b50013</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T09:46:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not parse d/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/commit/f04b57822a9fa613095dc32b7abe8190a8952c3c">f04b5782</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T09:51:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Attempt to point watch file to Github failed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/commit/882bd2b4c324dbeb7e33af8e2641df156a444a47">882bd2b4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T10:00:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/hisat2/compare/94a6bf8aaee7c662e4cd4abe8a1b4ae54afdbca3...882bd2b4c324dbeb7e33af8e2641df156a444a47#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hisat2 (2.1.0-2) unstable; urgency=medium</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"></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"> * Team upload.</span>
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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="plaintext"> * debhelper 11</span>
</pre>
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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
</pre>
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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"> * Standards-Version: 4.2.1</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> * Fix wrong path for Perl interpreter</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"> * Do not parse d/changelog</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 24 Sep 2018 11:52:06 +0200</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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1
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">hisat2 (2.1.0-1) unstable; urgency=medium</span>
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2
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Team upload</span>
</pre>
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</li>
<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/hisat2/compare/94a6bf8aaee7c662e4cd4abe8a1b4ae54afdbca3...882bd2b4c324dbeb7e33af8e2641df156a444a47#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/hisat2/compare/94a6bf8aaee7c662e4cd4abe8a1b4ae54afdbca3...882bd2b4c324dbeb7e33af8e2641df156a444a47#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: hisat2</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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4
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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5
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 10),</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: science</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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7
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7
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> help2man,</span>
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8
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> pandoc,</span>
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9
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.0</span></span>
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<td class="diff-line-num old old_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/hisat2.git</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/hisat2.git</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/hisat2</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/hisat2.git</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Package: hisat2</span>
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16
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16
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: amd64 kfreebsd-amd64</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, python</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> ${perl:Depends},</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> python</span>
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18
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Description: graph-based alignment of short nucleotide reads to many genomes</span>
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19
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> HISAT2 is a fast and sensitive alignment program for mapping next-generation</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> sequencing reads (both DNA and RNA) to a population of human genomes (as well</span>
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<a href="https://salsa.debian.org/med-team/hisat2/compare/94a6bf8aaee7c662e4cd4abe8a1b4ae54afdbca3...882bd2b4c324dbeb7e33af8e2641df156a444a47#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">@@ -7,14 +7,16 @@ export TZ=UTC</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</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">DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</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">DATE=$(shell date --date=@$(SOURCE_DATE_EPOCH) '+%d %B %Y')</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">%:</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> make BUILD_HOST='Debian<span class="idiff left right"> ${DEBFLAVOR}</span>' \</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> BUILD_TIME="$(<span class="idiff left right">shell date --date=@`dpkg-parsechangelog --show-field Timestamp`</span>)" \</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> make BUILD_HOST='Debian' \</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> BUILD_TIME="$(<span class="idiff left right">DATE</span>)" \</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> all doc</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> help2man ./hisat2 --no-info --name \</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> 'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \</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">@@ -37,3 +39,8 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> help2man ./hisat2-inspect-s --name 'HISAT2 index inspector, small index binary' \</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> --no-info > debian/hisat2-inspect-s.1</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">override_dh_install:</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> dh_install</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> done</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/hisat2/compare/94a6bf8aaee7c662e4cd4abe8a1b4ae54afdbca3...882bd2b4c324dbeb7e33af8e2641df156a444a47#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</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">version=4</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">opts="pasv,repack,compression=xz" \</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-([0-9.]+)-source.zip</span>
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4
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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"># Download tarball is very strangely named on Github - this will not work</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"># https://github.com/infphilo/hisat2/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span></pre>
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