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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/ampliconnoise">Debian Med / ampliconnoise</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/ampliconnoise/-/commit/7b399baf00dbc106af0232a4a35d5813d66de88c">7b399baf</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-07-24T08:12:40+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove now unneeded copyright paragraph
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<strong><a href="https://salsa.debian.org/med-team/ampliconnoise/-/commit/f610172d632ad865d420cf54ca43952f405189c6">f610172d</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-07-24T08:24:23+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Revert extra binary package since remaining data has a bearable size - with xz compression its even less.
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<h4>8 changed files:</h4>
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debian/ampliconnoise-examples.install
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debian/ampliconnoise.examples
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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debian/rules
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debian/source/include-binaries
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="e961207f5c3a9c88bd3a4b70b1e0fe53fe7069e5">
<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/83bf76b9337419b4e1cc3d053fecff08d755964e...f610172d632ad865d420cf54ca43952f405189c6#e961207f5c3a9c88bd3a4b70b1e0fe53fe7069e5"><strong>debian/ampliconnoise-examples.install</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tests</span><span class="o" style="font-weight: 600;">/</span><span class="nx">Run</span><span class="o" style="font-weight: 600;">.</span><span class="nx">sh</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">ampliconnoise</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="php"><span class="nx">Test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">C005</span><span class="o" style="font-weight: 600;">.</span><span class="nx">dat</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">ampliconnoise</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span></pre>
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<li id="00c567be1ab57aa69bd8a2b4b25526ebf509f18e">
<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/83bf76b9337419b4e1cc3d053fecff08d755964e...f610172d632ad865d420cf54ca43952f405189c6#00c567be1ab57aa69bd8a2b4b25526ebf509f18e"><strong>debian/ampliconnoise.examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/Run.sh</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Test/C005.dat</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/83bf76b9337419b4e1cc3d053fecff08d755964e...f610172d632ad865d420cf54ca43952f405189c6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,6 @@ ampliconnoise (1.29-9) unstable; urgency=medium</td>
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<td class="diff-line-num old_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"> * Trim trailing whitespace.</span>
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<td class="diff-line-num old_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"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> * New binary package featuring example data for testing</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> -- Pranav Ballaney <ballaneypranav@gmail.com> Sun, 19 Jul 2020 13:06:00 +0530</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/83bf76b9337419b4e1cc3d053fecff08d755964e...f610172d632ad865d420cf54ca43952f405189c6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<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">@@ -32,22 +32,3 @@ Description: removal of noise from 454 sequenced PCR amplicons</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> Previously there was a standalone "Pyronoise" by the same authors and</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> this package includes an updated version. There is also a "Denoiser"</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> in Qiime which is related but distinct.</span></pre>
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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: ampliconnoise-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: ampliconnoise</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">Description: removal of noise from 454 sequenced PCR amplicons (example data)</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> AmpliconNoise is a package of applications to clean up high-throughput</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> sequence data. It consists of three main parts:</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> Pyronoise - does flowgram-based clustering to spot misreads</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> SeqNoise - removes PCR point mutations</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> Perseus - removes PCR chimeras without the need for a set of reference</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> sequences</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> Previously there was a standalone "Pyronoise" by the same authors and</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> this package includes an updated version. There is also a "Denoiser"</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> in Qiime which is related but distinct.</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 ampliconnoise.</span></pre>
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<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/83bf76b9337419b4e1cc3d053fecff08d755964e...f610172d632ad865d420cf54ca43952f405189c6#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">@@ -11,13 +11,6 @@ Files: debian/*</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Copyright: © Tim Booth <tbooth@ceh.ac.uk></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">License: GPL-3</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Files: debian/tests/ref/*</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Copyright: 2020 Pranav Ballaney <ballaneypranav@gmail.com></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">License: GPL-3</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Comment: These files were generated by running Test/C005.dat</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> through AmpliconNoise as described in debian/tests/run-unit-test,</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> as a comparison reference for autopkgtests.</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">License: GPL-3</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> This library is free software; you can redistribute it and/or</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> modify it under the terms of the GNU Lesser General Public</span>
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<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/83bf76b9337419b4e1cc3d053fecff08d755964e...f610172d632ad865d420cf54ca43952f405189c6#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" 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">@@ -33,4 +33,6 @@ override_dh_installman:</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"> <span class="k" style="font-weight: 600;">done</span> <span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"></span>
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="nl">override_dh_compress</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># Use xz compression for data file to shrink size even more</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="make"> find debian <span class="nt" style="color: #000080;">-name</span> C005.dat <span class="nt" style="color: #000080;">-exec</span> xz <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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36
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"> dh_compress <span class="nt" style="color: #000080;">--exclude</span><span class="o" style="font-weight: 600;">=</span>.pdf</span></pre>
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<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/83bf76b9337419b4e1cc3d053fecff08d755964e...f610172d632ad865d420cf54ca43952f405189c6#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/tests/ref/C005.tar.xz</span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/ampliconnoise/-/compare/83bf76b9337419b4e1cc3d053fecff08d755964e...f610172d632ad865d420cf54ca43952f405189c6#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" 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="13" 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">@@ -13,7 +13,7 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"</td>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;"><span class="idiff left">gunzip</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-r</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">*</span></span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="idiff left">unxz </span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right">.xz</span></span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell">./Run.sh C005.dat</span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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