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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/minia">Debian Med / minia</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/minia/-/commit/6b22ed14f5abfed48cbd64304d8940e9690854c6">6b22ed14</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2021-02-16T16:14:36+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Wording. Added myself to uploaders.
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<strong><a href="https://salsa.debian.org/med-team/minia/-/commit/e30eaf4e8d414d7080712ce424c266f8ece3bdfd">e30eaf4e</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2021-02-16T19:33:20+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjust dep to patched version of gatb
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/minia/-/compare/0eaa42246bcb41e6d6f7e13e8e08e1f8f3dcb0ee...e30eaf4e8d414d7080712ce424c266f8ece3bdfd#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -3,14 +3,10 @@ minia (3.2.4-1) UNRELEASED; urgency=medium</td>
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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"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Adjusted build dependencies to patched version of gatb 1.4.2</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * d/rules - improved clean</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * d/watch - using regular releases again (up from 3.2.1 to 3.2.4)</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="LC8" class="line" lang="plaintext"> BLOCKER: FTBFS needs new gatb version</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> /usr/include/gatb/tools/math/Integer.hpp:84:71: required from ‘static void gatb::core::tools::math::IntegerTemplate<IntegerList>::apply(size_t, Parameter) [with Functor = MiniaFunctor; Parameter = Parameter; IntegerList = boost::mpl::vector4<mpl_::int_<32>, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> >; size_t = long unsigned int]’</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> /med-team/minia/src/Minia.cpp:170:65: required from here</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> /med-team/minia/src/Minia.cpp:312:62: error: ‘class gatb::core::debruijn::impl::GraphUnitigsTemplate<128>’ has no member named ‘_nbSolidKmers’</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"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Mon, 10 Aug 2020 19:16:26 +0200</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">minia (3.2.1+git20200522.4960a99-1) unstable; urgency=medium</span>
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<a href="https://salsa.debian.org/med-team/minia/-/compare/0eaa42246bcb41e6d6f7e13e8e08e1f8f3dcb0ee...e30eaf4e8d414d7080712ce424c266f8ece3bdfd#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: minia</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: Olivier Sallou <osallou@debian.org>,</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,9 +10,9 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> bc,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libboost-dev,</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> libgatbcore-dev (>= 1.4.<span class="idiff left right">1+git20191130.664696c</span>),</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> libgatbcore-dev (>= 1.4.<span class="idiff left right">2-7</span>),</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libhdf5-dev</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/minia</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/minia.git</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: http://minia.genouest.org/</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,9 +27,21 @@ Depends: ${misc:Depends},</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Recommends: samtools</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Suggests: bandage</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Description: short-read biological sequence assembler</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> Short-read DNA sequence assembler based on a de Bruijn graph,</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> capable of assembling a human genome on a desktop computer in a day.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> What was referred to as "next-generation" DNA sequencing up to</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> the year 2020 delivered only "short" reads up to ~600 base pairs</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> in length that would then have to be puzzled by random overlaps</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> in their sequence towards a complete genome. This is the genome</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> assembly. And there are many biological pitfalls on long stretches</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> of low complexity regions and copy number variations and other</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> sorts of redundancies that render this difficult.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> This package provides a short-read DNA sequence assembler based on a</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> de Bruijn graph, capable of assembling a human genome on a desktop</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> computer in a day.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> The output of Minia is a set of contigs, i.e. stretches of gap-free</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> linear overlaps of short reads. In the best possible case this is</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> a whole chromosome.</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> The output of Minia is a set of contigs.</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> Minia produces results of similar contiguity and accuracy to other</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> de Bruijn assemblers (e.g. Velvet).</span></pre>
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<a href="https://salsa.debian.org/med-team/minia/-/compare/0eaa42246bcb41e6d6f7e13e8e08e1f8f3dcb0ee...e30eaf4e8d414d7080712ce424c266f8ece3bdfd#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -11,3 +11,4 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">override_dh_clean:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> dh_clean</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> rm -f minia src/build_info.hpp</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> rm -rf obj-x86_64-linux-gnu src/build_info.hpp</span></pre>
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<a href="https://salsa.debian.org/med-team/minia/-/compare/0eaa42246bcb41e6d6f7e13e8e08e1f8f3dcb0ee...e30eaf4e8d414d7080712ce424c266f8ece3bdfd#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</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">@@ -3,6 +3,6 @@ version=4</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">https://github.com/GATB/minia/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"># Once upon a time, the released version was not compatible with gatb-core 1.4.1+git20191130.664696c+dfsg</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"># That is we sticked to latest Git commit back then.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"># That is w<span class="idiff left right">hy w</span>e sticked to latest Git commit back then.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">#opts="mode=git,pretty=3.2.1+git%cd.%h" \</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"># https://github.com/GATB/minia.git HEAD</span></pre>
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