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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/deepbinner">Debian Med / deepbinner</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/deepbinner/commit/c261fa929be1d01aeb91f19863454c8e3f82d38f">c261fa92</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-12-17T08:21:21Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Initial packaging
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/deepbinner/commit/fa5651fc6257427b2e75ef36d0bbf0950e3e5dfa">fa5651fc</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-12-17T08:25:48Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add todo list
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<h4>8 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
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debian/changelog
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<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
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debian/compat
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
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debian/control
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debian/copyright
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debian/rules
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debian/source/format
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debian/upstream/metadata
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debian/watch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/deepbinner/compare/e910ed671d00c25df1f241649b890a1454fbc520...fa5651fc6257427b2e75ef36d0bbf0950e3e5dfa#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">deepbinner (0.2.0-1) UNRELEASED; urgency=medium</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"> * Initial release (Closes: #<bug>)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> TODO:</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> 1. python3-tensorflow (see</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> https://lists.debian.org/debian-science/2018/12/msg00023.html )</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> 2. https://github.com/caseman/noise</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> 3. mappy (https://github.com/lh3/minimap2/tree/master/python)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -> minimap2 is in new</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 10 Dec 2018 13:34:46 +0100</span></pre>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/deepbinner/compare/e910ed671d00c25df1f241649b890a1454fbc520...fa5651fc6257427b2e75ef36d0bbf0950e3e5dfa#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/deepbinner/compare/e910ed671d00c25df1f241649b890a1454fbc520...fa5651fc6257427b2e75ef36d0bbf0950e3e5dfa#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: deepbinner</span>
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<pre style="margin: 0;">+<span id="LC2" 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="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python3,</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3-keras,</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python3-h5py,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python3-numpy,</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python3-edlib,</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"># python3-mappy,</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"># python3-noise,</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"># python3-tensorflow</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.2.1</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/deepbinner</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/deepbinner.git</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Homepage: https://github.com/rrwick/Deepbinner</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">Package: deepbinner</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Description: demultiplexing barcoded Oxford Nanopore sequencing reads</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> sequencing reads. It does this with a deep convolutional neural network</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> classifier, using many of the architectural advances that have proven</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> successful in image classification. Unlike other demultiplexers (e.g.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> Albacore and Porechop), Deepbinner identifies barcodes from the raw</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> signal (a.k.a. squiggle) which gives it greater sensitivity and fewer</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> unclassified reads.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> Reasons to use Deepbinner:</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> * To minimise the number of unclassified reads (use Deepbinner</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> by itself).</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> * To minimise the number of misclassified reads (use Deepbinner in</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> conjunction with Albacore demultiplexing).</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> * You plan on running signal-level downstream analyses, like</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> Nanopolish. Deepbinner can demultiplex the fast5 files which makes</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> this easier. Reasons to not use Deepbinner:</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> * You only have basecalled reads not the raw fast5 files (which</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> Deepbinner requires).</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> * You have a small/slow computer. Deepbinner is more computationally</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> intensive than Porechop.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> * You used a sequencing/barcoding kit other than the ones Deepbinner</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> was trained on.</span></pre>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/deepbinner/compare/e910ed671d00c25df1f241649b890a1454fbc520...fa5651fc6257427b2e75ef36d0bbf0950e3e5dfa#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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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: <pkg></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Source: <path_to_download></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Comment: **** Before manually editing this file you should give ****</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> scan-copyrights</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> **** available in cme + lib-config-model-dpkg-perl ****</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> **** package a try. For existing copyright files try ****</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> cme update dpkg-copyright</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">Files: *</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Copyright: © 20xx-20yy <upstream></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">License: <license></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/*</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Copyright: 2018 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">License: <license></span></pre>
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<a href="https://salsa.debian.org/med-team/deepbinner/compare/e910ed671d00c25df1f241649b890a1454fbc520...fa5651fc6257427b2e75ef36d0bbf0950e3e5dfa#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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2
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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"># DH_VERBOSE := 1</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</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">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"># DEB_SOURCE: the source package name</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"># DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"># DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM: the package's upstream version</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"># DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"># SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"># specified by <https://reproducible-builds.org/specs/source-date-epoch/></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></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="LC21" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">#override_dh_auto_test:</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"># do_stuff_for_testing</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">#endif</span></pre>
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<a href="https://salsa.debian.org/med-team/deepbinner/compare/e910ed671d00c25df1f241649b890a1454fbc520...fa5651fc6257427b2e75ef36d0bbf0950e3e5dfa#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/deepbinner/compare/e910ed671d00c25df1f241649b890a1454fbc520...fa5651fc6257427b2e75ef36d0bbf0950e3e5dfa#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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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: Ryan R Wick and Louise M Judd and Kathryn E Holt</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Title: "Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks"</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Journal: bioRxiv</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Year: 2018</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Volume: 14</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Number: 11</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Pages: e1006583</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> DOI: 10.1101/366526</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> PMID: 30458005</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> URL: https://www.biorxiv.org/content/early/2018/07/10/366526</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> eprint: https://www.biorxiv.org/content/biorxiv/early/2018/07/10/366526.full.pdf</span></pre>
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<a href="https://salsa.debian.org/med-team/deepbinner/compare/e910ed671d00c25df1f241649b890a1454fbc520...fa5651fc6257427b2e75ef36d0bbf0950e3e5dfa#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</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">https://github.com/rrwick/Deepbinner/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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