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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/t-coffee">Debian Med / t-coffee</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/t-coffee/commit/89cca1bf1dd87913927e242e38c4e08f94d6006d">89cca1bf</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-28T11:49:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add wrapper which sets HOME variable to $PWD in case HOME is not set
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/t-coffee/commit/9ad210165706d3d0e6b6f219a9b2e919703f3db8">9ad21016</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-28T11:54:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add NEWS.Debian to document the usage of a wrapper script
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/t-coffee/commit/931e227be1f62767e117fd952e9aa2bd27c09ea6">931e227b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-28T12:09:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix wrapper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/t-coffee/commit/fa629b584d7a085c415a8c270ec6d1d48ec58fb3">fa629b58</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-28T12:17:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Test suite fails when t_coffee is started via wrapper. Set PATH to find real t_coffee first.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/t-coffee/commit/52e126cc7d63867477bebbebf19b91cc71a91c02">52e126cc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-28T12:23:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop wrapper approach and instead make sure autopkgtest will set HOME variable to $PWD in case HOME is not set
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/t-coffee/commit/d9cb7de5089addc29c1c33538a68a2680a705e76">d9cb7de5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-28T12:26:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#d5d84e7420ab1baa0ac969a0116f7081fca3c48d">
<span class="new-file">
+
debian/bin/NEWS.Debian
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</li>
<li class="file-stats">
<a href="#27e120862259c5d6313d95668d5ffaa9e0b68404">
<span class="new-file">
+
debian/bin/README
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<li class="file-stats">
<a href="#075edc2a4a27727ba135c4e31db09f847a373816">
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+
debian/bin/t_coffee
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#34184d8ec6855dd10adb9645cf3b65b8adad7431">
debian/t-coffee.install
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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</ul>
<h4>Changes:</h4>
<li id="d5d84e7420ab1baa0ac969a0116f7081fca3c48d">
<a href="https://salsa.debian.org/med-team/t-coffee/compare/9cffa995e4603e396054062c6f3dbff1568bf243...d9cb7de5089addc29c1c33538a68a2680a705e76#d5d84e7420ab1baa0ac969a0116f7081fca3c48d"><strong>debian/bin/NEWS.Debian</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">t-coffee (11.00.8cbe486-8) 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"> As documented in bug #716373 (https://bugs.debian.org/716373) and</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"> #909530 (https://bugs.debian.org/909530) the t_coffee variable trows</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"> Segmentation Fault when HOME environment variable is not set. Since</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> some limited environments like autopkgtest chroot might not set HOME</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> t_coffee is now started via a wrapper shell script which will set</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> HOME to $PWD.</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"> -- Andreas Tille <tille@debian.org> Fri, 28 Sep 2018 13:13:33 +0200</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span></pre>
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</li>
<li id="27e120862259c5d6313d95668d5ffaa9e0b68404">
<a href="https://salsa.debian.org/med-team/t-coffee/compare/9cffa995e4603e396054062c6f3dbff1568bf243...d9cb7de5089addc29c1c33538a68a2680a705e76#27e120862259c5d6313d95668d5ffaa9e0b68404"><strong>debian/bin/README</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">This wrapper approach was done to always guarantee a HOME dir.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Unfortunately this approach did not worked well together with the</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">test suite.</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">Lets live with the "problem" that users really need to set a</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">HOME dir and at least make sure that the test suite will set one.</span></pre>
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<li id="075edc2a4a27727ba135c4e31db09f847a373816">
<a href="https://salsa.debian.org/med-team/t-coffee/compare/9cffa995e4603e396054062c6f3dbff1568bf243...d9cb7de5089addc29c1c33538a68a2680a705e76#075edc2a4a27727ba135c4e31db09f847a373816"><strong>debian/bin/t_coffee</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;"># t_coffee really needs $HOME variable set.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Since limited environments like autopkgtest chroots do not necessarily</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># set this variable this is set here to $PWD if it is not set.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">HOME</span><span class="k" style="font-weight: 600;">:-</span><span class="nv" style="color: teal;">$PWD</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: teal;">real_t_coffee_path</span><span class="o" style="font-weight: 600;">=</span>/usr/lib/t-coffee</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: teal;">real_t_coffee</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$real_t_coffee_path</span>/t_coffee</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># set $PATH to find real t_coffee before this wrapper. Otherwise test suite fails when started via wrapper</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">PATH</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$real_t_coffee_path</span><span class="s2" style="color: #d14;">:</span><span class="nv" style="color: teal;">$PATH</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-x</span> <span class="nv" style="color: teal;">$real_t_coffee</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="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>t_coffee <span class="nv" style="color: teal;">$@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Broken installation. Wrapper </span><span class="nv" style="color: teal;">$0</span><span class="s2" style="color: #d14;"> can not find </span><span class="nv" style="color: teal;">$real_t_coffee</span><span class="s2" style="color: #d14;"> ."</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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<a href="https://salsa.debian.org/med-team/t-coffee/compare/9cffa995e4603e396054062c6f3dbff1568bf243...d9cb7de5089addc29c1c33538a68a2680a705e76#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">t-coffee (11.00.8cbe486-8) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">t-coffee (11.00.8cbe486-8) <span class="idiff left right">unstable</span>; 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"> * Deal with "Segmentation fault" in exit of mayhem patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Closes: #909530</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Make sure autopkgtest will set HOME variable to $PWD in case HOME</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> is not set</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 28 Sep 2018 1<span class="idiff left right">3:13:33</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 28 Sep 2018 1<span class="idiff left right">4:24:07</span> +0200</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">t-coffee (11.00.8cbe486-7) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/t-coffee/compare/9cffa995e4603e396054062c6f3dbff1568bf243...d9cb7de5089addc29c1c33538a68a2680a705e76#34184d8ec6855dd10adb9645cf3b65b8adad7431"><strong>debian/t-coffee.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="nx">t_coffee_source</span><span class="o" style="font-weight: 600;">/</span><span class="nx">t_coffee</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">/</span></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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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">t_coffee_source</span><span class="o" style="font-weight: 600;">/</span><span class="nx">t_coffee</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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<a href="https://salsa.debian.org/med-team/t-coffee/compare/9cffa995e4603e396054062c6f3dbff1568bf243...d9cb7de5089addc29c1c33538a68a2680a705e76#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="12" 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>
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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">@@ -12,6 +12,9 @@ cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell">find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-name</span> <span class="s2" style="color: #d14;">"*.gz"</span> <span class="nt" style="color: navy;">-exec</span> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Make sure HOME is set in environment (see bug #909530)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">HOME</span><span class="k" style="font-weight: 600;">:-</span><span class="nv" style="color: teal;">$PWD</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell">t_coffee sample_seq1.fasta </span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell">t_coffee sample_seq1.fasta <span class="nt" style="color: navy;">-mode</span> quickaln </span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell">t_coffee sample_seq1.fasta <span class="nt" style="color: navy;">-mode</span> quickaln <span class="nt" style="color: navy;">-ndiag</span><span class="o" style="font-weight: 600;">=</span>10 </span>
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