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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/42b79ebdc89e88f8de708151b2e773185af42b84">42b79ebd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-04T21:00:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sibelia/commit/4dc66a483115b2aef1333897b9661d9368ddbc15">4dc66a48</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-04T21:01:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sibelia/commit/83edc701542a61fb7d078c50781496a2d534e8c7">83edc701</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-04T21:01:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sibelia/commit/f16847f3fc18f50338218a04241bcdc2f06def1e">f16847f3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-04T21:02:52+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Really upload to new
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sibelia/compare/34087e25af090e70107f741112624dc0358198eb...f16847f3fc18f50338218a04241bcdc2f06def1e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" 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">@@ -2,4 +2,4 @@ sibelia (3.0.7+dfsg-1) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #922377)</span>
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<td class="diff-line-num new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Fri, 15 Feb 2019 11:15:2</span>6 +0100</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Sat, 04 Jan 2020 21:01:3</span>6 +0100</span></pre>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/sibelia/compare/34087e25af090e70107f741112624dc0358198eb...f16847f3fc18f50338218a04241bcdc2f06def1e#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">12</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/sibelia/compare/34087e25af090e70107f741112624dc0358198eb...f16847f3fc18f50338218a04241bcdc2f06def1e#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" 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">@@ -2,11 +2,12 @@ Source: sibelia</td>
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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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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: non-free/science</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">XS-Autobuild: no</span>
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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="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 12~</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> cmake,</span>
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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">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libdivsufsort-dev</span>
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<td class="diff-line-num new_line old" data-linenumber="10" 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">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3.0</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/sibelia</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/sibelia.git</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: http://bioinf.spbau.ru/sibelia</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">@@ -34,7 +35,7 @@ Description: comparative genomics tool</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Package: sibelia-examples</span>
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<pre style="margin: 0;"> <span id="LC37" 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 class="idiff left right">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Description: comparative genomics tool (example data)</span>
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<pre style="margin: 0;"> <span id="LC40" 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="LC41" class="line" lang="plaintext"> It assists biologists in analysing the genomic variations that correlate</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">@@ -50,24 +51,3 @@ Description: comparative genomics tool (example data)</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> 3) rearrangements that transform one genome to other genomes.</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> This package contains example data for sibelia.</span></pre>
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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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71
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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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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/sibelia/compare/34087e25af090e70107f741112624dc0358198eb...f16847f3fc18f50338218a04241bcdc2f06def1e#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><span class="idiff left right"> </span>- Author: ></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- Author: ></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> Ilya Minkin and Anand Patel and Mikhail Kolmogorov and Nikolay Vyahhi and</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Son Pham</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> <span class="idiff left right"> </span>Title: ></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> Closely Related Microbial Genomes</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> <span class="idiff left right"> </span>Journal: Lecture Notes in Computer Science</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right"> </span>Year: 2013</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> <span class="idiff left right"> </span>DOI: 10.1007/978-3-642-40453-5_17</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right"> </span>URL: https://link.springer.com/chapter/10.1007/978-3-642-40453-5_17</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Journal: Lecture Notes in Computer Science</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Year: 2013</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> DOI: 10.1007/978-3-642-40453-5_17</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> URL: https://link.springer.com/chapter/10.1007/978-3-642-40453-5_17</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Registry:</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> - Name: bio.tools</span>
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<td class="diff-line-num old old_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> Entry: sibelia</span>
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<td class="diff-line-num old old_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> - Name: OMICtools</span>
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<td class="diff-line-num old old_line" data-linenumber="16" 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">
16
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<td class="diff-line-num new_line old" data-linenumber="13" 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">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> Entry: OMICS_11719</span>
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<td class="diff-line-num old old_line" data-linenumber="17" 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">
17
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<td class="diff-line-num new_line old" data-linenumber="13" 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">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> - Nane: conda:bioconda</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<td class="diff-line-num new_line old" data-linenumber="13" 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">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> Entry: sibelia</span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> - Name: SciCrunch</span>
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20
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<td class="diff-line-num new_line old" data-linenumber="13" 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">
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> Entry: NA</span></pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">- Name: bio.tools</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Entry: sibelia</span>
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<td class="diff-line-num new old_line" data-linenumber="21" 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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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">- Name: OMICtools</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Entry: OMICS_11719</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">- Nane: conda:bioconda</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> Entry: sibelia</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">- Name: SciCrunch</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Entry: NA</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Bug-Database: https://github.com/bioinf/Sibelia/issues</span></pre>
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