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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/sibelia">Debian Med / sibelia</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sibelia/commit/18f3e725ad9e51c3d8589aa1825c83b416d17113">18f3e725</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-02-14T16:49:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Spit into different binary packages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sibelia/commit/e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453">e81d4a8b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-02-14T21:57:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest
</pre>
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<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
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debian/README.test
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
debian/createmanpages
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<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="deleted-file">
−
debian/manpages
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#5175a5a502d58155dbbdbc6913c364792413cede">
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debian/sibelia-annotate.install
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<li class="file-stats">
<a href="#5637dc86a5223c0a60edae208e88dc4a3907bf60">
debian/lintian-overrides
→
debian/sibelia-annotate.lintian-overrides
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<li class="file-stats">
<a href="#53927efbce538bea92c2177268cb3e48d47a9c04">
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debian/sibelia-annotate.manpages
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<li class="file-stats">
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debian/sibelia-examples.install
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<li class="file-stats">
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debian/sibelia.docs
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debian/sibelia.install
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<a href="#0b80abb20667cec56c7a1ac84c41ee3a45958926">
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debian/sibelia.links
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debian/sibelia.lintian-overrides
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<li class="file-stats">
<a href="#7f3507834f09fbd8c0fb51f90f42243f45c34770">
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debian/sibelia.manpages
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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debian/tests/control
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#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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<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="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
</pre>
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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="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">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></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="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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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></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="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>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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="17" 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">@@ -17,6 +17,7 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> lagan</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Suggests: sibelia-examples</span>
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<td class="diff-line-num new_line" data-linenumber="21" 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="LC21" class="line" lang="plaintext">Description: comparative genomics tool</span>
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<td class="diff-line-num old_line" data-linenumber="21" 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="diff-line-num new_line" data-linenumber="22" 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="LC22" class="line" lang="plaintext"> Sibelia (Synteny Block ExpLoration tool) is a comparative genomics tool:</span>
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<td class="diff-line-num old_line" data-linenumber="22" 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="diff-line-num new_line" data-linenumber="23" 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="LC23" class="line" lang="plaintext"> It assists biologists in analysing the genomic variations that correlate</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" 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="31" 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">@@ -30,3 +31,43 @@ Description: comparative genomics tool</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> 1) shared regions,</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> 2) regions that present in one group of genomes but not in others,</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> 3) rearrangements that transform one genome to other genomes.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Package: sibelia-examples</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Description: comparative genomics tool (example data)</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> Sibelia (Synteny Block ExpLoration tool) is a comparative genomics tool:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> It assists biologists in analysing the genomic variations that correlate</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> with pathogens, or the genomic changes that help microorganisms adapt in</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> different environments. Sibelia will also be helpful for the</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> evolutionary and genome rearrangement studies for multiple strains of</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> microorganisms.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> Sibelia is useful in finding:</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> 1) shared regions,</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> 2) regions that present in one group of genomes but not in others,</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> 3) rearrangements that transform one genome to other genomes.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> This package contains example data for sibelia.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Package: sibelia-annotate</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> openjdk-11-jre | default-jre</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">Description: comparative genomics tool (annotation tool using snpEFF)</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> Sibelia (Synteny Block ExpLoration tool) is a comparative genomics tool:</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> It assists biologists in analysing the genomic variations that correlate</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> with pathogens, or the genomic changes that help microorganisms adapt in</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> different environments. Sibelia will also be helpful for the</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> evolutionary and genome rearrangement studies for multiple strains of</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> microorganisms.</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> Sibelia is useful in finding:</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> 1) shared regions,</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> 2) regions that present in one group of genomes but not in others,</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> 3) rearrangements that transform one genome to other genomes.</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> This package contains an annotation tool using snpEFF.</span></pre>
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<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</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">@@ -30,7 +30,10 @@ help2man --no-info --no-discard-stderr \</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$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="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;">></span> debian/sibelia.manpages <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="sh" style="color: #d14;">debian/C*.1</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="sh" style="color: #d14;">debian/S*.1</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="no" style="color: teal;">EOT</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC38" 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: teal;">EOT</span></span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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<li id="68e0b13744e158347bfd74ebaaca667435f07d14">
<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong>
deleted
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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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<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#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">@@ -10,13 +10,15 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh $@ --sourcedirectory=src</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">override_dh_installdocs:</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> dh_installdocs</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> mv debian/$(DEB_SOURCE)/usr/share/Sibelia/doc/* debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> rmdir debian/$(DEB_SOURCE)/usr/share/Sibelia/doc</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> dh_link usr/share/doc/$(DEB_SOURCE) usr/share/Sibelia/doc</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> find debian -name LICENSE.txt -delete</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> find debian -name INSTALL.md -delete</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> dh_installman</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> mkdir -p debian/$(DEB_SOURCE)-annotate//usr/share/man/man1</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> mv debian/$(DEB_SOURCE)-annotate/usr/share/man/py/man1/snpEffAnnotate.1 debian/$(DEB_SOURCE)-annotate/usr/share/man/man1/snpEffAnnotate.py.1</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> rm -rf debian/$(DEB_SOURCE)-annotate/usr/share/man/py/</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> mv debian/$(DEB_SOURCE)/usr/share/man/py/man1/C-Sibelia.1 debian/$(DEB_SOURCE)/usr/share/man/man1/C-Sibelia.py.1</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> rm -rf debian/$(DEB_SOURCE)/usr/share/man/py</span></pre>
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<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#5175a5a502d58155dbbdbc6913c364792413cede"><strong>debian/sibelia-annotate.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">snpEffAnnotate</span><span class="o" style="font-weight: 600;">.</span><span class="nx">py</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">Sibelia</span><span class="o" style="font-weight: 600;">/</span><span class="nx">snpEff</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#5637dc86a5223c0a60edae208e88dc4a3907bf60"><strong>debian/lintian-overrides</strong>
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<strong>debian/sibelia-annotate.lintian-overrides</strong>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">sibelia: script-with-language-extension usr/bin/*.*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">sibelia<span class="idiff left right">-annotate</span>: script-with-language-extension usr/bin/*.*</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># this file should not be there in an official package - so just ignore the wrong place for now</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">sibelia: jar-not-in-usr-share usr/lib/Sibelia/snpEff/snpEff.jar</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">sibelia<span class="idiff left right">-annotate</span>: jar-not-in-usr-share usr/lib/Sibelia/snpEff/snpEff.jar</span></pre>
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<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#53927efbce538bea92c2177268cb3e48d47a9c04"><strong>debian/sibelia-annotate.manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/snpEffAnnotate.py.1</span></pre>
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<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#f120569828d5191182b1765dc1d70d93bf1b7abf"><strong>debian/sibelia-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><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">Sibelia</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</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">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">sibelia</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#64776b4ee4f7f36cc838d2a2977c4fb9ba0c8321"><strong>debian/sibelia.docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/Sibelia/doc/[A-Z]*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">C</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="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">S</span><span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><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">Sibelia</span><span class="o" style="font-weight: 600;">/</span><span class="nx">utils</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#0b80abb20667cec56c7a1ac84c41ee3a45958926"><strong>debian/sibelia.links</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/doc/sibelia usr/share/Sibelia/doc</span></pre>
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<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#f94623b98e80a759e4e055e0239d20e1e3eabb4f"><strong>debian/sibelia.lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">sibelia: script-with-language-extension usr/bin/*.*</span></pre>
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<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#7f3507834f09fbd8c0fb51f90f42243f45c34770"><strong>debian/sibelia.manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/C*.1</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/S*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#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-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/sibelia/compare/f8a1e981c23fdb90ba4e4aa8c2f2953e925318e0...e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453#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/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: navy;">-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: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span>sibelia</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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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="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="LC7" 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><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$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="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <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="LC12" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: navy;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>C-Sibelia/Staphylococcus_aureus</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">C-Sibelia.py NCTC8325.fasta RN4220.fasta</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span>/Sibelia/Helicobacter_pylori</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">Sibelia <span class="nt" style="color: navy;">-s</span> loose Helicobacter_pylori.fasta</span></pre>
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