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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/trace2dbest">Debian Med / trace2dbest</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/trace2dbest/commit/bf1444140bb63656c5a46d369727f818d2caedab">bf144414</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2018-05-22T21:21:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Initial packaging.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/trace2dbest/commit/d3874fe5d4ff5daf664cebee10fa5c60d19845d9">d3874fe5</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2018-05-22T21:58:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">First round of improvements.
</pre>
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<h4>10 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
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+
debian/changelog
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="new-file">
+
debian/compat
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
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debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
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debian/copyright
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
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debian/rules
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<a href="#53399f7f2dd7535c43cdcfa511a9c06044a9c238">
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debian/source/format
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<li class="file-stats">
<a href="#12ca7121650d68e347830c50e4cc140279bccd06">
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debian/trace2dbest-doc.doc-base
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debian/trace2dbest-doc.docs
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<li class="file-stats">
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debian/trace2dbest.install
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debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/trace2dbest/compare/c41da461abcc9e4a310030c2c4c55754f12c5beb...d3874fe5d4ff5daf664cebee10fa5c60d19845d9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">trace2dbest (3.0.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Initial release (closes: #899322)</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="plaintext"></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="plaintext"> -- Steffen Moeller <moeller@debian.org> Tue, 22 May 2018 19:23:13 +0200</span></pre>
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<br>
</li>
<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/trace2dbest/compare/c41da461abcc9e4a310030c2c4c55754f12c5beb...d3874fe5d4ff5daf664cebee10fa5c60d19845d9#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">10</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/trace2dbest/compare/c41da461abcc9e4a310030c2c4c55754f12c5beb...d3874fe5d4ff5daf664cebee10fa5c60d19845d9#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: trace2dbest</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Uploaders: Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 10)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.1.4</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Homepage: http://www.nematodes.org/bioinformatics/trace2dbEST/</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/trace2dbest.git</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/trace2dbest</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Package: trace2dbest</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Depends: ${misc:Depends}, perl</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Description: bulk submission of chromatogram data to dbEST</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> ESTs are short sequences derived from reverse-transcribed RNA.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Their abundances yield insights in the expression of genes across</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> tissues, support the discovery of new genes and allow one to assess</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> the coverage of whole genome sequencing projects. Public databases</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> like dbEST at the NCBI collect this data.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> trace2dbEST process raw sequenceing chromatograph trace files from</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> EST projects into quality-checked sequences, ready for submission to</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> dbEST. trace2dbEST guides you through the creation of all the necessary</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> files for submission of ESTs to dbEST. trace2dbest makes use of other</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> software (available free under academic licence) that you will need to</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> have installed, namely phred, cross_match and (optionally) BLAST.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Package: trace2dbest-doc</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Recommends: pdf-viewer|xpdf</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Description: Documentation and sample files for trace2dbest</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> Sequence files and user guide to trace2dbEST.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Name: trace2dbest</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Source: http://www.nematodes.org/downloads/software/trace2dbest/trace2dbest_3.0.1.tar.gz</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Files: *</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Copyright: 2005 Alasdair Anthony, Ralf Schmid <nematode.bioinf@ed.ac.uk></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">License: GPL-2.0</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Copyright: 2018 Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">License: GPL-2.0</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">License: GPL-2.0</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> This package is free software; you can redistribute it and/or modify</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> the Free Software Foundation; version 2 of the License.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> This package is distributed in the hope that it will be useful,</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> GNU General Public License for more details.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> You should have received a copy of the GNU General Public License</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> along with this program. If not, see <https://www.gnu.org/licenses/></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"> On Debian systems, the complete text of the GNU General</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/trace2dbest/compare/c41da461abcc9e4a310030c2c4c55754f12c5beb...d3874fe5d4ff5daf664cebee10fa5c60d19845d9#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> dh $@</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">override_dh_compress:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh_compress -X.pdf -X.gz</span></pre>
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<li id="53399f7f2dd7535c43cdcfa511a9c06044a9c238">
<a href="https://salsa.debian.org/med-team/trace2dbest/compare/c41da461abcc9e4a310030c2c4c55754f12c5beb...d3874fe5d4ff5daf664cebee10fa5c60d19845d9#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0 (quilt)</span></pre>
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<a href="https://salsa.debian.org/med-team/trace2dbest/compare/c41da461abcc9e4a310030c2c4c55754f12c5beb...d3874fe5d4ff5daf664cebee10fa5c60d19845d9#12ca7121650d68e347830c50e4cc140279bccd06"><strong>debian/trace2dbest-doc.doc-base</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Document: trace2dbest</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Title: User Guide to trace2dbest</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Author: Alasdair Anthony, Ralf Schmid, John Parkinson, Mark Blaxter</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Abstract: Guided tour to submitting bulk EST data</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Section: Science/Biology</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Format: PDF</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Files: /usr/share/doc/trace2dbest-doc/trace2dbest3.0_UG.pdf</span></pre>
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<a href="https://salsa.debian.org/med-team/trace2dbest/compare/c41da461abcc9e4a310030c2c4c55754f12c5beb...d3874fe5d4ff5daf664cebee10fa5c60d19845d9#1a05ae55fbca376f9a6a8863a79d7e143422c8b6"><strong>debian/trace2dbest-doc.docs</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">*.pdf</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">*.seq</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">example_traces.tar.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/trace2dbest/compare/c41da461abcc9e4a310030c2c4c55754f12c5beb...d3874fe5d4ff5daf664cebee10fa5c60d19845d9#9e7668384cc96c062a040dae221a46a667adeac9"><strong>debian/trace2dbest.install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="o" style="font-weight: 600;">*.</span><span class="nx">pl</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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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/trace2dbest/compare/c41da461abcc9e4a310030c2c4c55754f12c5beb...d3874fe5d4ff5daf664cebee10fa5c60d19845d9#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> - Author: John Parkinson and Alasdair Anthony and James Wasmuth and</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Ralf Schmid and Ann Hedley and Mark Blaxter</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Title: PartiGene—constructing partial genomes</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Journal: Bioinformatics</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Volume: 20</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Issue: 9</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Day: 12</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Month: 6</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Year: 2004</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> Pages: 1398–1404</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> URL: https://academic.oup.com/bioinformatics/article/20/9/1398/195483</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> DOI: 10.1093/bioinformatics/bth101</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> ePrint: "https://academic.oup.com/bioinformatics/article-pdf/\</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> 20/9/1398/490254/bth101.pdf"</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> - Author: Ralf Schmid and Mark Blaxter</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Year: 2009</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> Type: Book chapter</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> EST Processing: From Trace to Sequence</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Editor: John Parkinson</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> Booktitle: Expressed Sequence Tags (ESTs)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> Series: Methods in Molecular Biology (Methods and Protocols)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> Volume: 533</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> Publisher: Humana Press</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> ISBN: 978-1-58829-759-4</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> DOI: 10.1007/978-1-60327-136-3_9</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> - Name: OMICtools</span>
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<td class="diff-line-num new new_line" data-linenumber="30" 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="LC30" class="line" lang="plaintext"> Entry: NA</span>
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<td class="diff-line-num new new_line" data-linenumber="31" 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="LC31" class="line" lang="plaintext"> - Name: SciCrunch</span>
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<td class="diff-line-num new new_line" data-linenumber="32" 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="LC32" class="line" lang="plaintext"> Entry: NA</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> - Name: bio.tools</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> Entry: NA</span></pre>
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