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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/ssake">Debian Med / ssake</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ssake/commit/4d0ba79d056f7d283748591e9ebf098afb5cd503">4d0ba79d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-08T07:15:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix installation of tools, fix link in examples
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ssake/commit/4b5a562e631dc841744535f4b389ee41de42a661">4b5a562e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-08T07:15:15Z</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/ssake/commit/df3f02cf7f196564775a2b14be713c3e4d28b110">df3f02cf</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-08T07:15:15Z</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/ssake/commit/5a563ffac7814e6f85561cd64a8523d387599f03">5a563ffa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-08T07:15:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix broken interpreter definitions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ssake/commit/b5bbad071ef9e8cee6324e2c292bdc3a3ee9180d">b5bbad07</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-08T07:15:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depends: ssake
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ssake/commit/4b09f9d4cfde0bbf9e474b43ac6f565e34e29480">4b09f9d4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-08T07:15:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Avoid errors when trying to fix shebang line in shell scripts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ssake/commit/ef59a2202bec34462d71a58dd63943f4c2701447">ef59a220</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-08T07:15:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</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="#079c54eddbc87aa292308108372b106ea174ec6d">
<span class="new-file">
+
debian/ssake-examples.links
</span>
</a>
</li>
<li class="file-stats">
<a href="#acfffae9c11632bcf8708093f29aa2c21cf0173a">
debian/ssake.docs
</a>
</li>
<li class="file-stats">
<a href="#89d9af63a84e50aed892046337809d7b86277040">
debian/ssake.install
</a>
</li>
<li class="file-stats">
<a href="#f1abfbde5d9ea948f03db657c20ac09cd9641c9a">
<span class="new-file">
+
debian/ssake.links
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ssake/compare/36e0109715a98700073d6807a74c758bbf5623d8...ef59a2202bec34462d71a58dd63943f4c2701447#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">ssake (4.0-2) 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"> * Fix installation of tools</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="plaintext"> * Fix link in examples, Depends: ssake</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"> Closes: #910414</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"> * Point Vcs fields to salsa.debian.org</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"> * Standards-Version: 4.2.1</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"> * Fix broken interpreter definitions</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">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Avoid errors when trying to fix shebang line in shell scripts</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></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"> -- Andreas Tille <tille@debian.org> Mon, 08 Oct 2018 09:04:43 +0200</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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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">ssake (4.0-1) unstable; urgency=medium</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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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> * New upstream version</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/ssake/compare/36e0109715a98700073d6807a74c758bbf5623d8...ef59a2202bec34462d71a58dd63943f4c2701447#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,9 +6,9 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python-markdown</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.3</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/ssake.git</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/ssake.git</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/ssake</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/ssake.git</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: http://www.bcgsc.ca/platform/bioinfo/software/ssake</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">Package: ssake</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="29" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,8 +29,8 @@ Description: genomics application for assembling millions of very short DNA sequ</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Package: ssake-examples</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"><span class="idiff left right">Suggests:</span> ssake</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Depends: ${misc:Depends}<span class="idiff left right">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"><span class="idiff left right"> </span> ssake</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Description: example data for SSAKE, a genomic assembler of short reads</span>
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<td class="diff-line-num old_line" data-linenumber="35" 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="LC35" class="line" lang="plaintext"> This package contains test sequences for SSAKE, a genomics application for</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> assembling millions of very short DNA sequences.</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/ssake/compare/36e0109715a98700073d6807a74c758bbf5623d8...ef59a2202bec34462d71a58dd63943f4c2701447#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,13 +16,17 @@ DOCDIR := $(CURDIR)/debian/$(examples)/usr/share/doc/$(DEB_SOURCE)</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> cp -a SSAKE $(BINDIR)/ssake</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> cp -a tools/TQS.py $(BINDIR)/tqs</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> # Fix totally broken interpreter definitions</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> for pl in `grep -Rl '#!/home/.\+/perl' debian/*/usr/*` ; do \</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> sed -i '1s?^#!/home/.\+/perl?#!/usr/bin/perl?' $${pl} ; \</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> done</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> for sh in `grep -Rl '#!/usr/bin/bash' debian/*/usr/*` ; do \</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> sed -i '1s?^#!/usr/bin/bash?#!/bin/bash?' $${sh} ; \</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> done</span>
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20
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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21
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">override_dh_installexamples:</span>
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22
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> dh_installexamples</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> for sh in $(DOCDIR)/examples/*.sh ; do \</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> sed -i '1 i #!/bin/sh' $${sh} ; \</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> done</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> find $(DOCDIR)/examples -name "*.sh" -type f -exec sed -i '1 i #!/bin/sh' \{\} \;</span>
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26
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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27
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">override_dh_installdocs:</span>
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28
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> dh_installdocs</span>
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<a href="https://salsa.debian.org/med-team/ssake/compare/36e0109715a98700073d6807a74c758bbf5623d8...ef59a2202bec34462d71a58dd63943f4c2701447#079c54eddbc87aa292308108372b106ea174ec6d"><strong>debian/ssake-examples.links</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/ssake/runSSAKE.sh usr/share/doc/ssake/examples/runSSAKE.sh</span></pre>
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<a href="https://salsa.debian.org/med-team/ssake/compare/36e0109715a98700073d6807a74c758bbf5623d8...ef59a2202bec34462d71a58dd63943f4c2701447#acfffae9c11632bcf8708093f29aa2c21cf0173a"><strong>debian/ssake.docs</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">tools/TQS.readme</span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tools/*readme</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">tools/*README</span></pre>
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<a href="https://salsa.debian.org/med-team/ssake/compare/36e0109715a98700073d6807a74c758bbf5623d8...ef59a2202bec34462d71a58dd63943f4c2701447#89d9af63a84e50aed892046337809d7b86277040"><strong>debian/ssake.install</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">tools</span><span class="o" style="font-weight: 600;">/</span><span class="p">[</span><span class="nx">mn</span><span class="p">]</span><span class="o" style="font-weight: 600;">*.</span><span class="nx">pl</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">ssake</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">tools</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">pl</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">ssake</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">tools</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">py</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">ssake</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="nx">tools</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">sh</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">ssake</span></span></pre>
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<li id="f1abfbde5d9ea948f03db657c20ac09cd9641c9a">
<a href="https://salsa.debian.org/med-team/ssake/compare/36e0109715a98700073d6807a74c758bbf5623d8...ef59a2202bec34462d71a58dd63943f4c2701447#f1abfbde5d9ea948f03db657c20ac09cd9641c9a"><strong>debian/ssake.links</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/ssake/TQS.py usr/bin/tqs</span></pre>
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