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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/hmmer2">Debian Med / hmmer2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hmmer2/commit/1a1e497df7d1b116854409c29efcae390015e403">1a1e497d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-11T18:09:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop hmmer2-pvm package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hmmer2/commit/e0bfa4d092605df3716b05ef1c9a14efcba80d11">e0bfa4d0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-11T18:10:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix install path
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hmmer2/commit/a0d40a6126c4aa34489a11f0246682b5c3f07917">a0d40a61</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-11T18:22:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix names
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hmmer2/commit/1b03ee93455c2d0671791975beaf3f737bf2dd11">1b03ee93</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-11T18:23:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">libhmmer2-dev package drops static lib
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hmmer2/commit/8b923271487055c4c896266c0abff2235855f30d">8b923271</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-11T18:24:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix doc installation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hmmer2/commit/e8e828b135bc5fd7855253eea5e3ac3deb680306">e8e828b1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-11T18:28:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">No upstream changelog
</pre>
</li>
</ul>
<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<span class="deleted-file">
−
debian/docs
</span>
</a>
</li>
<li class="file-stats">
<a href="#7d580d971bfbd4cacdff97dfdae3af6bd6c1ad1a">
<span class="deleted-file">
−
debian/hmmer2-pvm.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#ab8cc773f538aa5e5acf84df137c457db5c4277d">
<span class="deleted-file">
−
debian/hmmer2-pvm.README.Debian
</span>
</a>
</li>
<li class="file-stats">
<a href="#9861a02d45ee4e7ba67d7a2cb06e77edd34a3ffc">
<span class="deleted-file">
−
debian/hmmer2-pvm.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#13740aa742797030ed762b17662c49e56cd98ed6">
<span class="deleted-file">
−
debian/hmmer2-pvm.links
</span>
</a>
</li>
<li class="file-stats">
<a href="#9ba43b117ae039d053631c4c99e696820a50031c">
<span class="deleted-file">
−
debian/hmmer2-pvm.manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#a5cc705d84a614f7e6154a4803c92cd9fdb70510">
<span class="new-file">
+
debian/hmmer2.docs
</span>
</a>
</li>
<li class="file-stats">
<a href="#56306df12f3685cdab0b853c5e962f21cd749b32">
debian/libhmmer2-dev.install
</a>
</li>
<li class="file-stats">
<a href="#af5e13ec7db0b92fee10569b5904cd0fb8b966a6">
<span class="new-file">
+
debian/patches/fix_install.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" 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>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" 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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,6 +7,9 @@ hmmer2 (2.5j+dfsg-1) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num old_line" data-linenumber="7" 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">
7
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<td class="diff-line-num new_line" data-linenumber="7" 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * New upstream version</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="8" 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">
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<td class="diff-line-num new_line" data-linenumber="8" 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * debhelper 12</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="9" 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">
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<td class="diff-line-num new_line" data-linenumber="9" 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Standards-Version: 4.3.0</span>
</pre>
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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="plaintext"> * Drop hmmer2-pvm package</span>
</pre>
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<td class="diff-line-num new old_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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<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="plaintext"> * libhmmer2-dev package drops static lib (this is not automatically</span>
</pre>
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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="plaintext"> generated by upstream any more)</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="13" 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="11" 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">
11
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<td class="diff-line-num new_line" data-linenumber="14" 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 11 Jan 2019 15:43:07 +0100</span>
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12
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
</pre>
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<br>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" 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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,8 +21,7 @@ Architecture: any</td>
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21
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC21" class="line" lang="mosel"><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="p">${</span><span class="n" style="color: #333;">shlibs</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">misc</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">biosquid</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="mosel"><span class="n" style="color: #333;">Suggests</span><span class="p">:</span> <span class="n" style="color: #333;">hmmer2</span><span class="p">-</span><span class="n" style="color: #333;">doc</span> <span class="p">(>=</span> <span class="p">${</span><span class="n" style="color: #333;">source</span><span class="p">:</span><span class="k" style="font-weight: 600;">Version</span><span class="p">}),</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="mosel"> <span class="n" style="color: #333;">hmmer2</span><span class="p">-</span><span class="n" style="color: #333;">pvm</span> <span class="p">(>=</span> <span class="p">${</span><span class="n" style="color: #333;">binary</span><span class="p">:</span><span class="k" style="font-weight: 600;">Version</span><span class="p">})</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="mosel"><span class="n" style="color: #333;">Suggests</span><span class="p">:</span> <span class="n" style="color: #333;">hmmer2</span><span class="p">-</span><span class="n" style="color: #333;">doc</span> <span class="p">(>=</span> <span class="p">${</span><span class="n" style="color: #333;">source</span><span class="p">:</span><span class="k" style="font-weight: 600;">Version</span><span class="p">})</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">profile</span> <span class="n" style="color: #333;">hidden</span> <span class="n" style="color: #333;">Markov</span> <span class="n" style="color: #333;">models</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">protein</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">analysis</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="mosel"> <span class="n" style="color: #333;">HMMER</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">implementation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">profile</span> <span class="n" style="color: #333;">hidden</span> <span class="n" style="color: #333;">Markov</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">methods</span> <span class="n" style="color: #333;">for</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="mosel"> <span class="n" style="color: #333;">sensitive</span> <span class="n" style="color: #333;">searches</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">biological</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">databases</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">sequence</span></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">@@ -33,24 +32,6 @@ Description: profile hidden Markov models for protein sequence analysis</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="mosel"> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">database</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">find</span> <span class="p">(</span><span class="k" style="font-weight: 600;">and</span><span class="p">/</span><span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">align</span><span class="p">)</span> <span class="n" style="color: #333;">additional</span> <span class="n" style="color: #333;">homologues</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="mosel"> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">family</span><span class="p">.</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Package</span><span class="p">:</span> <span class="n" style="color: #333;">hmmer2</span><span class="p">-</span><span class="n" style="color: #333;">pvm</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="mosel"><span class="n" style="color: #333;">Architecture</span><span class="p">:</span> <span class="n" style="color: #333;">any</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="mosel"><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="p">${</span><span class="n" style="color: #333;">shlibs</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">misc</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="mosel"> <span class="n" style="color: #333;">pvm</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="mosel"><span class="n" style="color: #333;">Suggests</span><span class="p">:</span> <span class="n" style="color: #333;">hmmer2</span><span class="p">-</span><span class="n" style="color: #333;">doc</span> <span class="p">(>=</span> <span class="p">${</span><span class="n" style="color: #333;">binary</span><span class="p">:</span><span class="k" style="font-weight: 600;">Version</span><span class="p">})</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">HMMER</span> <span class="n" style="color: #333;">programs</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">PVM</span> <span class="p">(</span><span class="n" style="color: #333;">Parallel</span> <span class="n" style="color: #333;">Virtual</span> <span class="n" style="color: #333;">Machine</span><span class="p">)</span> <span class="n" style="color: #333;">support</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="mosel"> <span class="n" style="color: #333;">HMMER</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">implementation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">profile</span> <span class="n" style="color: #333;">hidden</span> <span class="n" style="color: #333;">Markov</span> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">methods</span> <span class="n" style="color: #333;">for</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="mosel"> <span class="n" style="color: #333;">sensitive</span> <span class="n" style="color: #333;">searches</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">biological</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">databases</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">sequence</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="mosel"> <span class="n" style="color: #333;">alignments</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">queries</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="mosel"> <span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="mosel"> <span class="n" style="color: #333;">Given</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">alignment</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">input</span><span class="p">,</span> <span class="n" style="color: #333;">HMMER</span> <span class="n" style="color: #333;">builds</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">statistical</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">model</span> <span class="n" style="color: #333;">called</span> <span class="n" style="color: #333;">a</span> <span class="s2" style="color: #d14;">"hidden Markov model"</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">can</span> <span class="k" style="font-weight: 600;">then</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">query</span> <span class="n" style="color: #333;">into</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="mosel"> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">database</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">find</span> <span class="p">(</span><span class="k" style="font-weight: 600;">and</span><span class="p">/</span><span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">align</span><span class="p">)</span> <span class="n" style="color: #333;">additional</span> <span class="n" style="color: #333;">homologues</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="mosel"> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">family</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="mosel"> <span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="mosel"> <span class="n" style="color: #333;">This</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">contains</span> <span class="n" style="color: #333;">HMMER</span> <span class="n" style="color: #333;">programs</span> <span class="n" style="color: #333;">compiled</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">PVM</span> <span class="n" style="color: #333;">support</span><span class="p">.</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Package</span><span class="p">:</span> <span class="n" style="color: #333;">hmmer2</span><span class="p">-</span><span class="n" style="color: #333;">doc</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="mosel"><span class="n" style="color: #333;">Architecture</span><span class="p">:</span> <span class="n" style="color: #333;">all</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="mosel"><span class="n" style="color: #333;">Section</span><span class="p">:</span> <span class="n" style="color: #333;">doc</span></span>
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<a href="https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">NOTES</span></pre>
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<a href="https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#7d580d971bfbd4cacdff97dfdae3af6bd6c1ad1a"><strong>debian/hmmer2-pvm.1</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH HMMER-PVM 1 "Tue, 08 Aug 2006 20:00:00 -0300"</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">hmmer2-pvm \- HMMER utilities for PVM clusters</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">.SH DESCRIPTION</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Information on how to use the programs</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">.B hmmcalibrate-pvm</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">,</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">.B hmmpfam-pvm</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">and</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">.B hmmsearch-pvm</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">is available on the section "Configuring a PVM cluster for HMMER" (page 15) at the User's Guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf).</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">.SH SEE ALSO</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">.BR hmmer2 (1),</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">.BR hmmer (1)</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">HMMER was written by Sean Eddy.</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>,</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">for the Debian project (but may be used by others).</span></pre>
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<a href="https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#ab8cc773f538aa5e5acf84df137c457db5c4277d"><strong>debian/hmmer2-pvm.README.Debian</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">hmmer2-pvm for Debian</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"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Please, read the section "Configuring a PVM cluster for HMMER" (page 15)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> at the User's Guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf), to see how to configure properly Hmmer on a PVM</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> cluster.</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="LC8" class="line" lang="plaintext"> -- Nelson A. de Oliveira <naoliv@gmail.com> Tue, 08 Aug 2006 23:07:12 -0300</span></pre>
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<a href="https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#9861a02d45ee4e7ba67d7a2cb06e77edd34a3ffc"><strong>debian/hmmer2-pvm.install</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">hmm2calibrate</span><span class="o" style="font-weight: 600;">-</span><span class="nx">pvm</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">hmm2pfam</span><span class="o" style="font-weight: 600;">-</span><span class="nx">pvm</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">hmm2search</span><span class="o" style="font-weight: 600;">-</span><span class="nx">pvm</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/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#13740aa742797030ed762b17662c49e56cd98ed6"><strong>debian/hmmer2-pvm.links</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2calibrate-pvm.1.gz</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2pfam-pvm.1.gz</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2search-pvm.1.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#9ba43b117ae039d053631c4c99e696820a50031c"><strong>debian/hmmer2-pvm.manpages</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/hmmer2-pvm.1</span></pre>
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<a href="https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#a5cc705d84a614f7e6154a4803c92cd9fdb70510"><strong>debian/hmmer2.docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Release-Notes</span></pre>
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<a href="https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#56306df12f3685cdab0b853c5e962f21cd749b32"><strong>debian/libhmmer2-dev.install</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">@@ -4,5 +4,5 @@ src/funcs.h usr/include/hmmer2</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">globals</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">hmmer2</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">postprob</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">hmmer2</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">structs</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">hmmer2</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">libhmmer</span><span class="o" style="font-weight: 600;">.</span><span class="nx">a</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="nx">DEB_HOST_MULTIARCH</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>src/libhmmer.a usr/lib/${DEB_HOST_MULTIARCH}</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">pkgconfig</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="nx">DEB_HOST_MULTIARCH</span><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#af5e13ec7db0b92fee10569b5904cd0fb8b966a6"><strong>debian/patches/fix_install.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Fri, 11 Jan 2019 15:43:07 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Do not duplicate prefix</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -55,13 +55,13 @@ src/libhmmer.a:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> # Prefix those paths with ${DESTDIR} (rarely used, usually null;</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> # may be set on a make command line when building contrib RPMs).</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> install:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mkdir -p ${DESTDIR}/$(BINDIR)/</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mkdir -p $(BINDIR)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> for file in $(PROGS) ; do\</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cp src/$$file "${DESTDIR}/$(BINDIR)/$$file""$(PROGSUFFIX)" ;\</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cp src/$$file "$(BINDIR)/$$file""$(PROGSUFFIX)" ;\</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> done</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> for file in hmmer2 $(ls documentation/man/); do\</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install -D documentation/man/$$file.man ${DESTDIR}/$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ install -D documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> done</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> # Reverses the steps of "make install". However, this should be handled</span></pre>
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<a href="https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_debian_packaged_biosquid.patch</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">build_libhmmer.a_with-fPIC.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">fix_typo.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">fix_install.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306#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">@@ -30,16 +30,13 @@ override_dh_auto_configure:</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> dh_auto_install -- prefix=$(CURDIR)/debian/tmp</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> # lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1:</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> rename 's/^hmm<span class="idiff left right">/hmm2</span>/;' $(CURDIR)/debian/tmp/bin/*</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> cd $(CURDIR)/debian/tmp/bin; rename 's/^hmm<span class="idiff left right">/hmm2</span>/;' *</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> cd $(CURDIR)/debian/tmp/share/man/man1; rename 's/^hmm<span class="idiff left right">/hmm2</span>/;' *</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> mv $(CURDIR)/debian/tmp/share/man/man1/hmm2er.1 $(CURDIR)/debian/tmp/share/man/man1/hmmer2.1</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> rename 's/^hmm<span class="idiff left right">(.+)2/hmm2$$1</span>/;' $(CURDIR)/debian/tmp/bin/*</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> cd $(CURDIR)/debian/tmp/bin; rename 's/^hmm<span class="idiff left right">(.+)2/hmm2$$1</span>/;' *</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> cd $(CURDIR)/debian/tmp/share/man/man1; rename 's/^hmm<span class="idiff left right">(.+)2/hmm2$$1</span>/;' *</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> <span class="idiff left right"># </span>mv $(CURDIR)/debian/tmp/share/man/man1/hmm2er.1 $(CURDIR)/debian/tmp/share/man/man1/hmmer2.1</span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> # lkajan: resolve man page hypen issue:</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' $(CURDIR)/debian/tmp/share/man/man1/*</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">override_dh_installchangelogs:</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> dh_installchangelogs -k 00README</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">override_dh_installexamples:</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> dh_installexamples</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> mkdir -p $(sampledir);</span>
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