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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pscan-tfbs">Debian Med / pscan-tfbs</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pscan-tfbs/commit/6fccae72f0b660acbdbdded9706381458aac473f">6fccae72</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-08T14:49:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unused template files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pscan-tfbs/commit/ba2a898f7936cff8b9de6966860f119412e43ce7">ba2a898f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-08T14:49:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">provide /usr/bin/pscan-tfbs to avoid file name conflict with pscan package and keep the original upstream name in /usr/lib/debian-med/bin/pscan
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pscan-tfbs/commit/e46d2547b102b62918cffdb0a7d170571058c263">e46d2547</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-08T14:49:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Explain name change in README.Debian
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pscan-tfbs/commit/59f809f672ebffe74340eafb02710c29c96c92bc">59f809f6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-08T14:49:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pscan-tfbs/commit/091bc024fd0f50121e2cf9f8cb3bb9e45896f276">091bc024</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-08T14:49:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
debian/README.Debian
</a>
</li>
<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="#68e0b13744e158347bfd74ebaaca667435f07d14">
debian/manpages
</a>
</li>
<li class="file-stats">
<a href="#9f537b3af81c9894ea2a45ae18144a7ef6612b90">
debian/pscan.1
→
debian/pscan-tfbs.1
</a>
</li>
<li class="file-stats">
<a href="#dd32db901fd3abe2b755aca0852dceb333bfe3b0">
debian/pscan-tfbs.install
</a>
</li>
<li class="file-stats">
<a href="#d48ae57884432bfe3ff50c574cb3676583f050fd">
<span class="new-file">
+
debian/pscan-tfbs.links
</span>
</a>
</li>
<li class="file-stats">
<a href="#3836a608f55cfd4741a176f056b47f1a5890bb46">
<span class="deleted-file">
−
debian/pscan.dirs
</span>
</a>
</li>
<li class="file-stats">
<a href="#e108a3d2cbfe9830d8e999bdc3662e834404cdae">
<span class="deleted-file">
−
debian/pscan.doc-base
</span>
</a>
</li>
<li class="file-stats">
<a href="#a6c37e820cd9caef496377b8eb55b928b80e8e2c">
<span class="deleted-file">
−
debian/pscan.install
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/pscan-tfbs/compare/f831163100447f738e1bec4edefbcdec33daa1b0...091bc024fd0f50121e2cf9f8cb3bb9e45896f276#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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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="LC1" class="line" lang="plaintext">pscan-tfbs for Debian</span>
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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="LC2" class="line" lang="plaintext">---------------------</span>
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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="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Please note that on Debian systems we can not use the name pscan because</span>
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<td class="diff-line-num new_line old" data-linenumber="4" 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="LC5" class="line" lang="plaintext">there is another package with the very same name. So the package is</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">renamed to pscan-tfbs.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Name conflict with pscan package</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">================================</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">We are facing a name clash in the Free Software universe and we have to</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">circumvent this somehow. In this package it is done was follows:</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"> 1. The pscan executable</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="plaintext"> /usr/lib/debian-med/bin/pscan</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> 2. The executable in the default PATH is</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="plaintext"> /usr/bin/pscan-tfbs</span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> (which is a symlink to the above executale)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">If you want to use pscan right from the command line just set the</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">PATH variable like</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> export PATH=/usr/lib/debian-med/bin:$PATH</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">If a user creates a file</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> ${HOME}/.blends</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">with the content</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"># Add Blend names here which should prepend its bin dir to PATH</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">debian-med</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">the med-config package automatically adds this PATH to the users</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">environment (when using bash).</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">JASPAR database</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">===============</span>
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7
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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8
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Pscan depends on a transcription factor binding site description. The </span>
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9
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">database "JASPAR" can be downloaded with the Debian 'getData' interface.</span>
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<a href="https://salsa.debian.org/med-team/pscan-tfbs/compare/f831163100447f738e1bec4edefbcdec33daa1b0...091bc024fd0f50121e2cf9f8cb3bb9e45896f276#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;">pscan</span><span class="p">-</span><span class="n" style="color: #333;">tfbs</span> <span class="p">(</span><span class="m" style="color: #099;">1.2.2</span><span class="p">-</span><span class="m" style="color: #099;">2</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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<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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Remove</span> <span class="n" style="color: #333;">unused</span> <span class="n" style="color: #333;">template</span> <span class="n" style="color: #333;">files</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">provide</span> <span class="p">/</span><span class="n" style="color: #333;">usr</span><span class="p">/</span><span class="n" style="color: #333;">bin</span><span class="p">/</span><span class="n" style="color: #333;">pscan</span><span class="p">-</span><span class="n" style="color: #333;">tfbs</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">avoid</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">name</span> <span class="n" style="color: #333;">conflict</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pscan</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">package</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">keep</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">original</span> <span class="n" style="color: #333;">upstream</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">in</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"> <span class="p">/</span><span class="n" style="color: #333;">usr</span><span class="p">/</span><span class="n" style="color: #333;">lib</span><span class="p">/</span><span class="n" style="color: #333;">debian</span><span class="p">-</span><span class="n" style="color: #333;">med</span><span class="p">/</span><span class="n" style="color: #333;">bin</span><span class="p">/</span><span class="n" style="color: #333;">pscan</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"> <span class="n" style="color: #333;">Closes</span><span class="p">:</span> <span class="p">#</span><span class="m" style="color: #099;">901039</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.1.4</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"></span>
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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;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p"><</span><span class="n" style="color: #333;">tille</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;">Fri</span><span class="p">,</span> <span class="m" style="color: #099;">08</span> <span class="n" style="color: #333;">Jun</span> <span class="m" style="color: #099;">2018</span> <span class="m" style="color: #099;">14</span><span class="p">:</span><span class="m" style="color: #099;">48</span><span class="p">:</span><span class="m" style="color: #099;">00</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"><span class="n" style="color: #333;">pscan</span><span class="p">-</span><span class="n" style="color: #333;">tfbs</span> <span class="p">(</span><span class="m" style="color: #099;">1.2.2</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;">low</span></span>
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2
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="mosel"> <span class="p">[</span> <span class="n" style="color: #333;">Steffen</span> <span class="n" style="color: #333;">Moeller</span> <span class="p">]</span></span>
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<a href="https://salsa.debian.org/med-team/pscan-tfbs/compare/f831163100447f738e1bec4edefbcdec33daa1b0...091bc024fd0f50121e2cf9f8cb3bb9e45896f276#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">@@ -5,7 +5,7 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 10),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> libgsl-dev</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">3</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pscan-tfbs</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pscan-tfbs.git</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Homepage: http://www.beaconlab.it/pscan</span>
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<a href="https://salsa.debian.org/med-team/pscan-tfbs/compare/f831163100447f738e1bec4edefbcdec33daa1b0...091bc024fd0f50121e2cf9f8cb3bb9e45896f276#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/<span class="idiff left right">pscan</span>.1</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/<span class="idiff left right">*</span>.1</span></pre>
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<a href="https://salsa.debian.org/med-team/pscan-tfbs/compare/f831163100447f738e1bec4edefbcdec33daa1b0...091bc024fd0f50121e2cf9f8cb3bb9e45896f276#9f537b3af81c9894ea2a45ae18144a7ef6612b90"><strong>debian/pscan.1</strong>
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<strong>debian/pscan-tfbs.1</strong>
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<a href="https://salsa.debian.org/med-team/pscan-tfbs/compare/f831163100447f738e1bec4edefbcdec33daa1b0...091bc024fd0f50121e2cf9f8cb3bb9e45896f276#dd32db901fd3abe2b755aca0852dceb333bfe3b0"><strong>debian/pscan-tfbs.install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">pscan</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx"><span class="idiff left right">bin</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">pscan</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx"><span class="idiff left">lib</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">debian</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nx"><span class="idiff">med</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">bin</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">/</span></span></span></pre>
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<a href="https://salsa.debian.org/med-team/pscan-tfbs/compare/f831163100447f738e1bec4edefbcdec33daa1b0...091bc024fd0f50121e2cf9f8cb3bb9e45896f276#d48ae57884432bfe3ff50c574cb3676583f050fd"><strong>debian/pscan-tfbs.links</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/lib/debian-med/bin/pscan usr/bin/pscan-tfbs</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># Also link the manpage to the Debian Med name space</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">usr/share/man/man1/pscan-tfbs.1.gz usr/lib/debian-med/share/man/man1/pscan.1.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/pscan-tfbs/compare/f831163100447f738e1bec4edefbcdec33daa1b0...091bc024fd0f50121e2cf9f8cb3bb9e45896f276#3836a608f55cfd4741a176f056b47f1a5890bb46"><strong>debian/pscan.dirs</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/bin</span></pre>
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<a href="https://salsa.debian.org/med-team/pscan-tfbs/compare/f831163100447f738e1bec4edefbcdec33daa1b0...091bc024fd0f50121e2cf9f8cb3bb9e45896f276#e108a3d2cbfe9830d8e999bdc3662e834404cdae"><strong>debian/pscan.doc-base</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Document: pscan</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Title: Debian pscan Manual</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Author: G.Pesole,</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> G.Pavesi <giulio.pavesi@unimi.it>,</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> F.Zambelli <federico.zambelli@unimi.it></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Abstract: The document resembles a UNIX man page.</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Format: text</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Files: /usr/share/doc/pscan/HELP.txt.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/pscan-tfbs/compare/f831163100447f738e1bec4edefbcdec33daa1b0...091bc024fd0f50121e2cf9f8cb3bb9e45896f276#a6c37e820cd9caef496377b8eb55b928b80e8e2c"><strong>debian/pscan.install</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">pscan</span> <span class="o" style="font-weight: 600;">/</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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