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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/kleborate">Debian Med / kleborate</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/commit/47d29ab58997aad455d4b11d321c8bbe3d50b4eb">47d29ab5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-27T10:53:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make sure Debian packaged kaptive will be found
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/commit/bba0a7611bebe6b36ac08a8210f5a1a87724a01c">bba0a761</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-27T10:53:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Also use kaptive-data which contains the needed .gbk files
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#aaf098af659f3693f6797564e506656574573468">
<span class="new-file">
+
debian/patches/use_debian_installed_kaptive.patch
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</li>
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/kleborate/compare/c0a759b5643a169207eb1cc72dce6760adef4779...bba0a7611bebe6b36ac08a8210f5a1a87724a01c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +21,8 @@ Depends: ${python3:Depends},</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> ${misc:Depends},</span>
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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"> ncbi-blast+,</span>
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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"> mash,</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> kaptive</span>
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<td class="diff-line-num new new_line" data-linenumber="24" 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="LC24" class="line" lang="plaintext"> kaptive,</span>
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<td class="diff-line-num new new_line" data-linenumber="25" 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="LC25" class="line" lang="plaintext"> kaptive-data</span>
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<td class="diff-line-num old_line" data-linenumber="25" 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="26" 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="LC26" class="line" lang="plaintext">Recommends: python3-biopython</span>
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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="plaintext">Description: tool to screen Klebsiella genome assemblies</span>
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<td class="diff-line-num new_line" data-linenumber="28" 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="LC28" class="line" lang="plaintext"> Kleborate is a tool to screen Klebsiella genome assemblies for:</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/kleborate/compare/c0a759b5643a169207eb1cc72dce6760adef4779...bba0a7611bebe6b36ac08a8210f5a1a87724a01c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">python3.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_get_resource_paths.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">use_debian_installed_kaptive.patch</span></pre>
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<li id="aaf098af659f3693f6797564e506656574573468">
<a href="https://salsa.debian.org/med-team/kleborate/compare/c0a759b5643a169207eb1cc72dce6760adef4779...bba0a7611bebe6b36ac08a8210f5a1a87724a01c#aaf098af659f3693f6797564e506656574573468"><strong>debian/patches/use_debian_installed_kaptive.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 24 Sep 2019 12:36:03 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Make sure Debian packaged kaptive will be found</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/kleborate/kleborate.py</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/kleborate/kleborate.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -353,13 +353,13 @@</span> def get_resource_paths():</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> def get_kaptive_paths():</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> this_file = os.path.realpath(__file__)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- kaptive_dir = os.path.join(os.path.dirname(os.path.dirname(this_file)), 'kaptive')</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ kaptive_dir = '/usr/bin'</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> if not os.path.isdir(kaptive_dir):</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> sys.exit('Error: could not find Kaptive directory. Did you git clone with --recursive?')</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> kaptive_py = os.path.join(kaptive_dir, 'kaptive.py')</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> if not os.path.isfile(kaptive_py):</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> sys.exit('Error: could not find kaptive.py')</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- db_dir = os.path.join(kaptive_dir, 'reference_database')</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ db_dir = '/usr/share/kaptive/reference_database'</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> kaptive_k_db = os.path.join(db_dir, 'Klebsiella_k_locus_primary_reference.gbk')</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> if not os.path.isfile(kaptive_k_db):</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> sys.exit('Error: could not find Klebsiella_k_locus_primary_reference.gbk')</span></pre>
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