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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/kaptive">Debian Med / kaptive</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/commit/1cd87a9d8420842ad0ef6487b751ebd246aff9ce">1cd87a9d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-24T19:38:37Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest after adding packages with the needed data
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<h4>8 changed files:</h4>
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<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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<a href="#38b07791809c436e8541e411503b79c2e730e3c3">
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debian/kaptive-data.install
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<li class="file-stats">
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debian/kaptive-example.install
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debian/kaptive.docs
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debian/kaptive.install
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debian/tests/control
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debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/kaptive/commit/1cd87a9d8420842ad0ef6487b751ebd246aff9ce#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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></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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<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 class="nx">You</span> <span class="nx">need</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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"><span class="nx">to</span> <span class="nx">install</span> <span class="nx">kaptive</span><span class="o" style="font-weight: 600;">-</span><span class="nx">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="nx">kaptive</span><span class="o" style="font-weight: 600;">-</span><span class="nx">example</span> <span class="nx">package</span> <span class="nx">before</span> <span class="nx">you</span> <span class="nx">can</span> <span class="nx">run</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC7" 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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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC9" 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 id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/kaptive/commit/1cd87a9d8420842ad0ef6487b751ebd246aff9ce#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,10 +14,13 @@ Vcs-Git: https://salsa.debian.org/med-team/kaptive.git</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://github.com/katholt/Kaptive</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Package: kaptive</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ny</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ll</span></span>
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<td class="diff-line-num old_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> python3-biopython</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> python3-biopython,</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> ncbi-blast+</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Suggests: kaptive-data,</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> kaptive-example</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Description: obtain information about K and O types for Klebsiella genome assemblies</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> Kaptive reports information about K and O types for Klebsiella genome</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> assemblies.</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">@@ -45,3 +48,72 @@ Description: obtain information about K and O types for Klebsiella genome assemb</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> to you! Very poor assemblies can confound the results, so be sure to</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> closely examine any case where the locus sequence in your assembly is</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> broken into multiple pieces.</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">Package: kaptive-data</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Enhances: kaptive</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Description: reference data for kaptive for Klebsiella genome assemblies</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> Kaptive reports information about K and O types for Klebsiella genome</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> assemblies.</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> Given a novel genome and a database of known loci (K or O), Kaptive will</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> help a user to decide whether their sample has a known or novel locus.</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> It carries out the following for each input assembly:</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> * BLAST for all known locus nucleotide sequences (using blastn) to</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> identify the best match ('best' defined as having the highest</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> coverage).</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> * Extract the region(s) of the assembly which correspond to the BLAST</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> hits (i.e. the locus sequence in the assembly) and save it to a</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> FASTA file.</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> * BLAST for all known locus genes (using tblastn) to identify which</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> expected genes (genes in the best matching locus) are present/missing</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> and whether any unexpected genes (genes from other loci) are present.</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> * Output a summary to a table file.</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> .</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> In cases where your input assembly closely matches a known locus,</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> Kaptive should make that obvious. When your assembly has a novel type,</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> that too should be clear. However, Kaptive cannot reliably extract or</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> annotate locus sequences for totally novel types - if it indicates a</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> novel locus is present then extracting and annotating the sequence is up</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> to you! Very poor assemblies can confound the results, so be sure to</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> closely examine any case where the locus sequence in your assembly is</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> broken into multiple pieces.</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> This package contains a reference database. Its not necessarily used</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> to run kaptive since you can use your own database.</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">Package: kaptive-example</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">Enhances: kaptive</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">Description: example data for kaptive for Klebsiella genome assemblies</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> Kaptive reports information about K and O types for Klebsiella genome</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> assemblies.</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> .</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> Given a novel genome and a database of known loci (K or O), Kaptive will</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> help a user to decide whether their sample has a known or novel locus.</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> It carries out the following for each input assembly:</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> .</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> * BLAST for all known locus nucleotide sequences (using blastn) to</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> identify the best match ('best' defined as having the highest</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> coverage).</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> * Extract the region(s) of the assembly which correspond to the BLAST</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> hits (i.e. the locus sequence in the assembly) and save it to a</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> FASTA file.</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> * BLAST for all known locus genes (using tblastn) to identify which</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> expected genes (genes in the best matching locus) are present/missing</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> and whether any unexpected genes (genes from other loci) are present.</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> * Output a summary to a table file.</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> .</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> In cases where your input assembly closely matches a known locus,</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> Kaptive should make that obvious. When your assembly has a novel type,</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> that too should be clear. However, Kaptive cannot reliably extract or</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> annotate locus sequences for totally novel types - if it indicates a</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> novel locus is present then extracting and annotating the sequence is up</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> to you! Very poor assemblies can confound the results, so be sure to</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> closely examine any case where the locus sequence in your assembly is</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> broken into multiple pieces.</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> This package contains some example data.</span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/commit/1cd87a9d8420842ad0ef6487b751ebd246aff9ce#38b07791809c436e8541e411503b79c2e730e3c3"><strong>debian/kaptive-data.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">reference_database</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">kaptive</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/commit/1cd87a9d8420842ad0ef6487b751ebd246aff9ce#1246925af782cf03ff72f809371050f9060f7e06"><strong>debian/kaptive-example.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">sample_data</span><span class="o" style="font-weight: 600;">/*</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">kaptive</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/commit/1cd87a9d8420842ad0ef6487b751ebd246aff9ce#26fdc582b4348e56e2be30a88d01d5433ba522e1"><strong>debian/kaptive.docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">README*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/README.test</span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/commit/1cd87a9d8420842ad0ef6487b751ebd246aff9ce#1642cefec3a60648eab36823f7a30dfd23d49231"><strong>debian/kaptive.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">kaptive</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">bin</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/commit/1cd87a9d8420842ad0ef6487b751ebd246aff9ce#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/kaptive/commit/1cd87a9d8420842ad0ef6487b751ebd246aff9ce#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: #000080;">-e</span></span>
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3
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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: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>kaptive</span>
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5
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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="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 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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<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="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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8
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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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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>
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15
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<pre style="margin: 0;">+<span id="LC15" 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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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">kaptive.py <span class="nt" style="color: #000080;">-a</span> exact_match.fasta <span class="nt" style="color: #000080;">-k</span> /usr/share/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/reference_database/Klebsiella_k_locus_primary_reference.gbk <span class="nt" style="color: #000080;">-o</span> output/test</span></pre>
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