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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-biopython">Debian Med / python-biopython</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/commit/0bf3df35757f0b83f658ff23043e3c94e72635df">0bf3df35</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-10T09:18:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update build-deps for better testing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/commit/677988d3406273113dd6bc554bd450f9ff30f93b">677988d3</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-10T09:18:41Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Skip test_mmtf{,_online}
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/commit/47e21414316713499cb3a6a9f90aa0ae95e1a61c">47e21414</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-10T09:28:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">i386: build-dep on raxml for testing purposes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/commit/d5df812fb2ba7839ff08f1c87c140cc9e2a4ff88">d5df812f</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-10T09:28:41Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">enable the python3 tests
</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
<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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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-biopython/compare/7ca7ec9227df4669ce36d62bfd307a36427dbb42...d5df812fb2ba7839ff08f1c87c140cc9e2a4ff88#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.75</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">UNRELEASED</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"></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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Team</span> <span class="n" style="color: #333;">upload</span><span class="p">.</span></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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Skip</span> <span class="n" style="color: #333;">PDB_ResidueDepth</span> <span class="n" style="color: #333;">test</span><span class="p">,</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">mgltools</span><span class="p">.</span><span class="n" style="color: #333;">scripps</span><span class="p">.</span><span class="n" style="color: #333;">edu</span><span class="p">/</span><span class="n" style="color: #333;">packages</span><span class="p">/</span><span class="n" style="color: #333;">MSMS</span></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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">yet</span> <span class="n" style="color: #333;">packaged</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">Debian</span></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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Skip</span> <span class="n" style="color: #333;">test_mmtf</span><span class="p">{,</span><span class="n" style="color: #333;">_online</span><span class="p">}</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">rcsb</span><span class="p">/</span><span class="n" style="color: #333;">mmtf</span><span class="p">-</span><span class="n" style="color: #333;">python</span> <span class="n" style="color: #333;">is</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">yet</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"> <span class="n" style="color: #333;">packaged</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">Debian</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">dependencies</span><span class="p">:</span> <span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">unittest2</span><span class="p">,</span> <span class="n" style="color: #333;">python</span><span class="p">{,</span><span class="m" style="color: #099;">3</span><span class="p">}-</span><span class="n" style="color: #333;">networkx</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="mosel"> <span class="n" style="color: #333;">samtools</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">i386</span><span class="p">:</span> <span class="n" style="color: #333;">build</span><span class="p">-</span><span class="n" style="color: #333;">dep</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">raxml</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">testing</span> <span class="n" style="color: #333;">purposes</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Fix</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">ignoring</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">errors</span> <span class="n" style="color: #333;">so</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">python3</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">still</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="mosel"> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Michael</span> <span class="n" style="color: #333;">R</span><span class="p">.</span> <span class="n" style="color: #333;">Crusoe</span> <span class="p"><</span><span class="n" style="color: #333;">michael</span><span class="p">.</span><span class="n" style="color: #333;">crusoe</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">></span> <span class="n" style="color: #333;">Tue</span><span class="p">,</span> <span class="m" style="color: #099;">10</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">2019</span> <span class="m" style="color: #099;">10</span><span class="p">:</span><span class="m" style="color: #099;">12</span><span class="p">:</span><span class="m" style="color: #099;">10</span> <span class="p">+</span><span class="m" style="color: #099;">0100</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.75</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">New</span> <span class="n" style="color: #333;">upstream</span> <span class="k" style="font-weight: 600;">version</span></span>
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<a href="https://salsa.debian.org/med-team/python-biopython/compare/7ca7ec9227df4669ce36d62bfd307a36427dbb42...d5df812fb2ba7839ff08f1c87c140cc9e2a4ff88#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -31,6 +31,8 @@ Build-Depends: debhelper-compat (= 12),</td>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> phyml [any-amd64 any-i386 arm64 armhf sparc64],</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> prank,</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> probcons,</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> python-networkx,</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> python3-networkx,</span>
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34
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> python-mysqldb,</span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> python3-mysqldb,</span>
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36
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> python-matplotlib,</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">@@ -47,7 +49,9 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> python3-scipy,</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> python-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> raxml [any-amd64],</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> python-unittest2,</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> raxml [any-amd64 any-i386],</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> samtools [alpha arm64 armel armhf hppa ia64 m68k mips mips64el mipsel powerpc powerpcspe ppc64 ppc64el s390x sh4 sparc64],</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> t-coffee,</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> wise,</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> python3-pygments</span>
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<a href="https://salsa.debian.org/med-team/python-biopython/compare/7ca7ec9227df4669ce36d62bfd307a36427dbb42...d5df812fb2ba7839ff08f1c87c140cc9e2a4ff88#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">@@ -26,7 +26,7 @@ EXCLUDENONFREE=PAML_tools EmbossPhylipNew</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"># avoid testing tools that are not packaged for Debian yet (or will never be packaged since they might be outdated)</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"># This would not trigger a failure but bloats the build log with irrelevant noise</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">EXCLUDENOTPACKAGED=MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">EXCLUDENOTPACKAGED=MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool<span class="idiff left right"> PDB_ResidueDepth mmtf mmtf_online</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"># avoid amd64 only tools on other architectures</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">ifeq ($(BUILDARCH),amd64)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="109" 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">@@ -109,7 +109,7 @@ else</td>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> cp -a Doc/examples {build_dir}/Doc; \</span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext"> cp -a Tests {build_dir}; \</span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext"> cd {build_dir}/Tests; \</span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext"> env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline<span class="idiff left right">' || true</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline<span class="idiff left right"> || true'</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext"> mv Tests_avoid/* Tests</span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext"> rmdir Tests_avoid</span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext">endif</span>
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