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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/flye">Debian Med / flye</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/flye/-/commit/f7951c6556efa92895dd20a61ed1467c5cc342e1">f7951c65</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-28T08:30:02+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Create some hopefully sensible test once flye is supposed to work
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<strong><a href="https://salsa.debian.org/med-team/flye/-/commit/deb022a09f4f81555cd814e80fb1d573600d7e77">deb022a0</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-28T08:30:52+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add todo
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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debian/tests/data/get
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/flye/-/compare/d6c7122a1772197bbf454abf0efb4efff35c6687...deb022a09f4f81555cd814e80fb1d573600d7e77#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">flye (2.7.1+dfsg-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: #962292)</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"> <span class="idiff left right">Wait for https://github.com/fenderglass/Flye/issues/275 to be resolved.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <span class="idiff left right">TODO: See https://github.com/fenderglass/Flye/issues/275</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <span class="idiff left right"> Wait until minimap2 patch is applied</span></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"> -- Andreas Tille <tille@debian.org> Fri, 05 Jun 2020 15:05:08 +0200</span></pre>
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<li id="9bf2a2dfe7c558515faf61ee2ebf6555b79a85d7">
<a href="https://salsa.debian.org/med-team/flye/-/compare/d6c7122a1772197bbf454abf0efb4efff35c6687...deb022a09f4f81555cd814e80fb1d573600d7e77#9bf2a2dfe7c558515faf61ee2ebf6555b79a85d7"><strong>debian/tests/data/get</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># see docs/USAGE.md</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell">wget https://zenodo.org/record/1172816/files/E.coli_PacBio_40x.fasta</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># FIXME: I'm hesitating to include such a big dataset here</span></span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/flye/-/compare/d6c7122a1772197bbf454abf0efb4efff35c6687...deb022a09f4f81555cd814e80fb1d573600d7e77#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -6,14 +6,21 @@ pkg=#PACKAGENAME#</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"></span>
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17
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span></pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">REALLYRUNTEST</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"yes"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># From docs/USAGE.md:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">wget https://zenodo.org/record/1172816/files/E.coli_PacBio_40x.fasta</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">flye <span class="nt" style="color: #000080;">--pacbio-raw</span> E.coli_PacBio_40x.fasta <span class="nt" style="color: #000080;">--out-dir</span> out_pacbio <span class="nt" style="color: #000080;">--genome-size</span> 5m <span class="nt" style="color: #000080;">--threads</span> 4</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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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">wget https://zenodo.org/record/1172816/files/Loman_E.coli_MAP006-1_2D_50x.fasta</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">flye <span class="nt" style="color: #000080;">--nano-raw</span> Loman_E.coli_MAP006-1_2D_50x.fasta <span class="nt" style="color: #000080;">--out-dir</span> out_nano <span class="nt" style="color: #000080;">--genome-size</span> 5m <span class="nt" style="color: #000080;">--threads</span> 4</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>flye <span class="nt" style="color: #000080;">--help</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test is downloading large databases. Set "REALLYRUNTEST=yes" to run this test'</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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