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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/abacas">Debian Med / abacas</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/abacas/-/commit/56755113ed9f9ef0e464e0836f2dd7dc57e95a4b">56755113</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-05-28T20:25:01+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add binary:abacas-examples
Since we intend not to bloat user's machine with heavy files
</pre>
</li>
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<strong><a href="https://salsa.debian.org/med-team/abacas/-/commit/75d05f847b884c6259a1d1ac18f892ad65b81745">75d05f84</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-05-28T20:26:30+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Modify tests to use abacas-examples
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#1d4cf19bc05e174cce2e9ca1f9667aa602fcb298">
debian/examples
→
debian/abacas-examples.docs
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="1d4cf19bc05e174cce2e9ca1f9667aa602fcb298">
<a href="https://salsa.debian.org/med-team/abacas/-/compare/4e9d4f67aab28a99ab5f77f1e12f9a43a60606e9...75d05f847b884c6259a1d1ac18f892ad65b81745#1d4cf19bc05e174cce2e9ca1f9667aa602fcb298"><strong>debian/examples</strong>
→
<strong>debian/abacas-examples.docs</strong>
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<a href="https://salsa.debian.org/med-team/abacas/-/compare/4e9d4f67aab28a99ab5f77f1e12f9a43a60606e9...75d05f847b884c6259a1d1ac18f892ad65b81745#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<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">@@ -16,7 +16,7 @@ Architecture: all</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Depends: ${perl:Depends},</span>
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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"> mummer</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Recommends: primer3</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Recommends: primer3<span class="idiff left right">, abacas-examples</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Description: close gaps in genomic alignments from short reads</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> ABACAS (Algorithm Based Automatic Contiguation of Assembled Sequences)</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> intends to rapidly contiguate (align, order, orientate), visualize and</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" 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="32" 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">@@ -32,3 +32,16 @@ Description: close gaps in genomic alignments from short reads</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> identity between comparable blocks. Information on contigs such as the</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> orientation, percent identity, coverage and overlap with other contigs</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> can also be visualized by loading the outputted feature file on ACT.</span>
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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: abacas-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="LC38" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Enhances: abacas</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Description: sample data for abacas to close gaps in genomic alignments</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> ABACAS (Algorithm Based Automatic Contiguation of Assembled Sequences)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> intends to rapidly contiguate (align, order, orientate), visualize and</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> design primers to close gaps on shotgun assembled contigs based on a</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> reference sequence.</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"> This package contains a test data set as well as sample scripts</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> running some test suite provided by Debian also as autopkgtest.</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/abacas/-/compare/4e9d4f67aab28a99ab5f77f1e12f9a43a60606e9...75d05f847b884c6259a1d1ac18f892ad65b81745#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -8,7 +8,7 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then</td>
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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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> /usr/share/doc/<span class="k" style="font-weight: 600;"><span class="idiff left">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">pkg</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="idiff right">/</span>examples/<span class="k" style="font-weight: 600;">*</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> /usr/share/doc/<span class="idiff left right">abacas-</span>examples/<span class="k" style="font-weight: 600;">*</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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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="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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