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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/soapdenovo2">Debian Med / soapdenovo2</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/soapdenovo2/commit/ad5c6e10dd11bfe2cd51514f7c759631f5e6c99c">ad5c6e10</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2018-06-12T18:28:44+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest
</pre>
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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="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
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debian/source/include-binaries
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debian/tests/control
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
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debian/tests/run-unit-test
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debian/tests/test-data/SRR2480581.fastq.tar.gz
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/soapdenovo2/commit/ad5c6e10dd11bfe2cd51514f7c759631f5e6c99c#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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">_______________________________________</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">execution</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
</pre>
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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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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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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 id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/soapdenovo2/commit/ad5c6e10dd11bfe2cd51514f7c759631f5e6c99c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">soapdenovo2 (241+dfsg-3) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Liubov Chuprikova <chuprikovalv@gmail.com> Tue, 12 Jun 2018 17:35:14 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">soapdenovo2 (241+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * debian/upstream/metadata:</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/soapdenovo2/commit/ad5c6e10dd11bfe2cd51514f7c759631f5e6c99c#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -79,3 +79,21 @@ License: GPL-2+</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"> On Debian systems, the complete text of the GNU General</span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"> Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">Files: debian/tests/test-data/SRR2480581.fastq.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">Copyright: 1996-2018 NCBI</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">License: unrestricted</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> Databases of molecular data on the NCBI Web site include such examples as</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> nucleotide sequences (GenBank), protein sequences, macromolecular structures,</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> molecular variation, gene expression, and mapping data. They are designed to</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> provide and encourage access within the scientific community to sources of</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> current and comprehensive information. Therefore, NCBI itself places no</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> restrictions on the use or distribution of the data contained therein. Nor do</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> we accept data when the submitter has requested restrictions on reuse or</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> redistribution.</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">Comment:</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> The test data files contained in the archive are a small data set prepared</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> from the original SRA with accession number SRR2480581.</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> .</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> To download the original file you can use fastq-dump tool from SRA Toolkit:</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> fastq-dump --split-3 SRR2480581</span></pre>
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<a href="https://salsa.debian.org/med-team/soapdenovo2/commit/ad5c6e10dd11bfe2cd51514f7c759631f5e6c99c#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.md</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/test-data</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/README.test</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/test-data/SRR2480581.fastq.tar.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/soapdenovo2/commit/ad5c6e10dd11bfe2cd51514f7c759631f5e6c99c#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/soapdenovo2/commit/ad5c6e10dd11bfe2cd51514f7c759631f5e6c99c#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/sh -e</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"soapdenovo2"</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" 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;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</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;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test-data/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-xzvf</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz<span class="p">;</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Starting soapdenovo2-63mer test..."</span></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;">echo</span> <span class="s2" style="color: #d14;">">>>>>Step 1: pregraph"</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">soapdenovo2-63mer pregraph <span class="nt" style="color: navy;">-s</span> example.config <span class="nt" style="color: navy;">-o</span> graph</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.kmerFreq <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.edge.gz <span class="o" style="font-weight: 600;">]</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.preArc <span class="o" style="font-weight: 600;">]</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.vertex <span class="o" style="font-weight: 600;">]</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.preGraphBasic <span class="o" style="font-weight: 600;">]</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Step 2: contig"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">soapdenovo2-63mer contig <span class="nt" style="color: navy;">-g</span> graph</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.contig <span class="o" style="font-weight: 600;">]</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.Arc <span class="o" style="font-weight: 600;">]</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.updated.edge <span class="o" style="font-weight: 600;">]</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.ContigIndex <span class="o" style="font-weight: 600;">]</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Step 3: map"</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">soapdenovo2-63mer map <span class="nt" style="color: navy;">-s</span> example.config <span class="nt" style="color: navy;">-g</span> graph</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.peGrads <span class="o" style="font-weight: 600;">]</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.readOnContig.gz <span class="o" style="font-weight: 600;">]</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.readInGap.gz <span class="o" style="font-weight: 600;">]</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"></span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Step 4: scaff"</span></span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">soapdenovo2-63mer scaff <span class="nt" style="color: navy;">-g</span> graph</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.newContigIndex <span class="o" style="font-weight: 600;">]</span></span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.links <span class="o" style="font-weight: 600;">]</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.scaf_gap <span class="o" style="font-weight: 600;">]</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.scaf <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-e</span> graph.gapSeq <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> graph.scafSeq <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># soapdenovo2-127mer testing requires lots of memory->Skipped</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span></pre>
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