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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/sepp">Debian Med / sepp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/c4a6f4b73a5367a74797ee50ffd218a965daa73a">c4a6f4b7</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-26T10:41:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding dependency to ncbi-blast+
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/56030d08099413b7f3a5f56c2adaf4ac157fdc00">56030d08</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-26T10:41:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/edf70426efb401aeb2bc41021f75657ebed4e8a8">edf70426</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-26T10:47:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using Debian paths for executables
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/fb458d48ff3e8ff4729aed723fa572c5ce266d7d">fb458d48</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-26T10:49:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixing syntax error in lintian-overrides file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/46b0614b8068517473dc32f6df0ecadd33a629e6">46b0614b</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-26T10:53:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Handling the build of the two other jars
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/471e9300a3399e61f7358218711b91394f003d7a">471e9300</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-26T10:58:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Making conffiles placed into /etc
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/48f6e95b4f03a20631736e9711ef824433deaf00">48f6e95b</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-26T11:09:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Hacking for making build tests, errors still to be fixed
</pre>
</li>
</ul>
<h4>10 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="#68d8c5c6babbf5cf109b2584c454449dbff75772">
<span class="new-file">
+
debian/install
</span>
</a>
</li>
<li class="file-stats">
<a href="#8a5501661d0634356baa31697665b72b16f41f4d">
debian/patches/change_java_version_for_ant.patch
</a>
</li>
<li class="file-stats">
<a href="#3376dba004c17b9d80d1885abdb0f45aee93c34c">
<span class="new-file">
+
debian/patches/java_build.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#0fb2ebdf1422ca07aa40555402a7793da21fdefa">
debian/patches/use_debian_packaged_guppy_from_pplacer.patch
</a>
</li>
<li class="file-stats">
<a href="#0f49e705e7863393470071ea898d70d59fc2f2a3">
<span class="new-file">
+
debian/patches/use_etc_configuration_files.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#9979085cf4bd85f96bf1690f49b7194102a233f0">
debian/sepp.lintian-overrides
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sepp/-/compare/c458c31847f39900a4dae5ae07bf816d1c1f2a40...48f6e95b4f03a20631736e9711ef824433deaf00#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,7 +3,8 @@ sepp (4.3.10+dfsg-1) UNRELEASED; urgency=medium</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<bug>)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> TODO:</span>
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<td class="diff-line-num new_line" data-linenumber="5" 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" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> - See if split_sequences.py should be shipped.</span>
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<td class="diff-line-num old old_line" data-linenumber="6" 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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<td class="diff-line-num new_line old" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> - <span class="idiff left right">Call build-time tests in debian/rules</span>.</span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> - <span class="idiff left right">Debug build-time</span>.</span>
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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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> - Write manpages.</span>
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<td class="diff-line-num new old_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">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> - Write autopkgtests.</span>
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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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> <span class="idiff left right">Wed, 19 Aug 2020 11:02:08</span> +0200</span></pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> <span class="idiff left right">Sat, 26 Sep 2020 11:05:33</span> +0200</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/sepp/-/compare/c458c31847f39900a4dae5ae07bf816d1c1f2a40...48f6e95b4f03a20631736e9711ef824433deaf00#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: sepp</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Pierre Gruet <pgtdebian@free.fr></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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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">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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7
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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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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8
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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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3,</span>
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9
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<td class="diff-line-num new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-setuptools,</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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python3-dendropy,</span>
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10
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> pplacer,</span>
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11
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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">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> hmmer,</span>
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12
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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">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> ant,</span>
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13
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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"> libjenkins-json-java,</span>
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14
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<td class="diff-line-num new_line old" data-linenumber="16" 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="LC14" class="line" lang="plaintext"> libgoogle-gson-java</span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> libgoogle-gson-java,</span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> ncbi-blast+</span>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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16
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<td class="diff-line-num new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/sepp</span>
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<td class="diff-line-num old_line" data-linenumber="17" 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">
17
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<td class="diff-line-num new_line" data-linenumber="20" 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">
20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/sepp.git</span>
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<td class="diff-line-num old_line" data-linenumber="18" 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">
18
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<td class="diff-line-num 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">
21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Homepage: https://github.com/smirarab/sepp/</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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19
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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20
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Package: sepp</span>
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21
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<td class="diff-line-num new_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" 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="34" 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">@@ -30,7 +34,8 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> libcommons-beanutils-java,</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> libcommons-collections3-java,</span>
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32
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> libcommons-lang-java,</span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> libcommons-logging-java</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> libcommons-logging-java,</span>
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<td class="diff-line-num new new_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> ncbi-blast+</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Description: methods use ensembles of Hidden Markov Models (HMM)</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> The tools SEPP, TIPP, UPP and HIPPI implementing three methods use</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> ensembles of Hidden Markov Models (HMMs) in different ways, each</span>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/c458c31847f39900a4dae5ae07bf816d1c1f2a40...48f6e95b4f03a20631736e9711ef824433deaf00#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">main.config etc/sepp</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">tipp.config etc/sepp</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">upp.config etc/sepp</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">tools/merge/*JsonMerger.jar usr/share/sepp/</span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/c458c31847f39900a4dae5ae07bf816d1c1f2a40...48f6e95b4f03a20631736e9711ef824433deaf00#8a5501661d0634356baa31697665b72b16f41f4d"><strong>debian/patches/change_java_version_for_ant.patch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Pierre Gruet <pgtdebian@free.fr></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Date: Fri, 1<span class="idiff left right">4 Aug 2020 22:4</span>0:28 +0200</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Date: Fri, 1<span class="idiff left right">8 Sep 2020 22:3</span>0:28 +0200</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: More recent version of Java suppresses some warnings</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Origin: https://lists.debian.org/debian-med/2020/08/msg00104.html</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,3 +14,14 @@ Origin: https://lists.debian.org/debian-med/2020/08/msg00104.html</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> <classpath refid="classpath"/></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </javac></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> </target></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/merge/tipp.xml</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/merge/tipp.xml</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -29,7 +29,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> <target name="compile"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> <mkdir dir="${deploy.home}/classes"/></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <javac srcdir="src" destdir="${deploy.home}/classes" source="1.6" target="1.6" debug="on" ></span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <javac srcdir="src" destdir="${deploy.home}/classes" source="1.8" target="1.8" debug="on" ></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> <classpath refid="classpath"/></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </javac></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </target></span></pre>
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<li id="3376dba004c17b9d80d1885abdb0f45aee93c34c">
<a href="https://salsa.debian.org/med-team/sepp/-/compare/c458c31847f39900a4dae5ae07bf816d1c1f2a40...48f6e95b4f03a20631736e9711ef824433deaf00#3376dba004c17b9d80d1885abdb0f45aee93c34c"><strong>debian/patches/java_build.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Adapting the build.xml file of ant to Debian policy</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> There are no embedded jars to include.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> The classpath thus has to be changed to include Debian-packaged jars.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> The .java files should not be included in the target jars.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Last-Update: 2020-09-18</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">--- a/tools/merge/build.xml</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/merge/build.xml</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -44,12 +44,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> <attribute name="Main-Class" value="${main.class}" /> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> <!-- Finally, use the generated libs path --> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <attribute name="Class-Path" value="lib/*.jar" /> </span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <attribute name="Class-Path" value="/usr/share/java/jenkins-json-lib.jar /usr/share/java/gson.jar" /> </span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </manifest> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <zipgroupfileset dir="lib" includes="*.jar" /></span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <!--<fileset dir="lib" includes="*.jar"/> --></span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <fileset dir="${src.home}" includes="**/*.java"/> </span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </jar> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </target> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/merge/tipp.xml</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/merge/tipp.xml</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -44,12 +44,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> <attribute name="Main-Class" value="${main.class}" /> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> <!-- Finally, use the generated libs path --> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <attribute name="Class-Path" value="lib/*.jar" /> </span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <attribute name="Class-Path" value="/usr/share/java/jenkins-json-lib.jar /usr/share/java/gson.jar" /> </span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </manifest> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <zipgroupfileset dir="lib" includes="*.jar" /></span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <!--<fileset dir="lib" includes="*.jar"/> --></span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <fileset dir="${src.home}" includes="**/*.java"/> </span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </jar> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </target> </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/c458c31847f39900a4dae5ae07bf816d1c1f2a40...48f6e95b4f03a20631736e9711ef824433deaf00#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -2,3 +2,5 @@ setup.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">use_debian_packaged_guppy_from_pplacer.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">change_java_version_for_ant.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">json_collections.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">java_build.patch</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">use_etc_configuration_files.patch</span></pre>
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<li id="0fb2ebdf1422ca07aa40555402a7793da21fdefa">
<a href="https://salsa.debian.org/med-team/sepp/-/compare/c458c31847f39900a4dae5ae07bf816d1c1f2a40...48f6e95b4f03a20631736e9711ef824433deaf00#0fb2ebdf1422ca07aa40555402a7793da21fdefa"><strong>debian/patches/use_debian_packaged_guppy_from_pplacer.patch</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">@@ -46,3 +46,55 @@ Description: Use Debian packaged guppy and hmm*</td>
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46
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> </span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> def initialize_options(self):</span>
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48
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> """init options"""</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/unittest/testConfig.py</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/unittest/testConfig.py</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -93,7 +93,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> sys.argv = [sys.argv[0], "-c", get_data_path("configs/test2.config")]</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> # set pplacer filepath to a file shipped with the code base</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> options().pplacer.path = get_data_path(</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "../../../tools/bundled/Darwin/pplacer")</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "/usr/bin/pplacer")</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> assert (options().pplacer is not None and os.path.exists(</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> options().pplacer.path)), \</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="p">@@ -102,14 +102,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> options().pplacer.path)</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> options().hmmalign.path = get_data_path(</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "../../../tools/bundled/Darwin/hmmalign")</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "/usr/bin/hmmalign")</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> assert (options().hmmalign is not None and os.path.exists(</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> options().hmmalign.path)), \</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> ("main config file options not read properly, or nonexistent "</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> "binaries: hmmalign = %s" % options().hmmalign.path)</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> options().hmmsearch.path = get_data_path(</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "../../../tools/bundled/Darwin/hmmsearch")</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "/usr/bin/hmmsearch")</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> assert (options().hmmsearch is not None and os.path.exists(</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> options().hmmsearch.path)), \</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> ("main config file options not read properly, or nonexistent "</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/unittest/testMidpoint.py</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/unittest/testMidpoint.py</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="p">@@ -41,8 +41,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> suff_bit = ""</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> for prog in ['hmmalign', 'hmmbuild', 'hmmsearch', 'pplacer']:</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> setattr(self.x.options, prog, Namespace(</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- path=get_data_path("../../../tools/bundled/%s/%s%s" % (</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- platform.system(), prog, suff_bit))))</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ path=get_data_path("/usr/bin/" + prog)))</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> </span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> def setUp(self):</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> # ensure necessary settings are made</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/unittest/testSepp.py</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/unittest/testSepp.py</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="p">@@ -42,8 +42,7 @@</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> suff_bit = ""</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> for prog in ['hmmalign', 'hmmbuild', 'hmmsearch', 'pplacer']:</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> setattr(self.x.options, prog, Namespace(</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- path=get_data_path("../../../tools/bundled/%s/%s%s" % (</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- platform.system(), prog, suff_bit))))</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ path=get_data_path("/usr/bin/" + prog)))</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> </span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> def tearDown(self):</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> self.x.options.alignment_file.close()</span></pre>
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<li id="0f49e705e7863393470071ea898d70d59fc2f2a3">
<a href="https://salsa.debian.org/med-team/sepp/-/compare/c458c31847f39900a4dae5ae07bf816d1c1f2a40...48f6e95b4f03a20631736e9711ef824433deaf00#0f49e705e7863393470071ea898d70d59fc2f2a3"><strong>debian/patches/use_etc_configuration_files.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: using configuration files that are in /etc</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-09-19</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/run_tipp_tool.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/run_tipp_tool.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -43,9 +43,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> return args</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-root_p = open(os.path.join(os.path.split(</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.path.split(sepp.__file__)[0])[0], "home.path")).readlines()[0].strip()</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-tipp_config_path = os.path.join(root_p, "tipp.config")</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+tipp_config_path = "/etc/sepp/tipp.config"</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> def profile(input, gene, output, prefix, threshold):</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;">--- a/sepp/config.py</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;">+++ b/sepp/config.py</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -48,9 +48,7 @@</span></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"> _LOG = get_logger(__name__)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-root_p = open(os.path.join(os.path.split(</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.path.split(__file__)[0])[0], "home.path")).readlines()[0].strip()</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-main_config_path = os.path.join(root_p, "main.config")</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+main_config_path = "/etc/sepp/main.config"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> def set_main_config_path(filename):</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/sepp/ensemble.py</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/sepp/ensemble.py</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -161,7 +161,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> def augment_parser():</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sepp.config.set_main_config_path(os.path.expanduser("~/.sepp/upp.config"))</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sepp.config.set_main_config_path("/etc/sepp/upp.config")</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> parser = sepp.config.get_parser()</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> parser.description = (</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> "This script runs the UPP algorithm on set of sequences. A backbone "</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/sepp/exhaustive_tipp.py</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/sepp/exhaustive_tipp.py</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -483,12 +483,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> def augment_parser():</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- root_p = open(</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.path.join(</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.path.split(</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.path.split(</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __file__)[0])[0], "home.path")).readlines()[0].strip()</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tipp_config_path = os.path.join(root_p, "tipp.config")</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tipp_config_path = "/etc/sepp/tipp.config"</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> sepp.config.set_main_config_path(tipp_config_path)</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> # default_settings['DEF_P'] = (100 ,</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> # "Number of taxa (i.e. no decomposition)")</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/sepp/exhaustive_upp.py</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/sepp/exhaustive_upp.py</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="p">@@ -324,9 +324,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> def augment_parser():</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- root_p = open(os.path.join(os.path.split(</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.path.split(__file__)[0])[0], "home.path")).readlines()[0].strip()</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- upp_config_path = os.path.join(root_p, "upp.config")</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ upp_config_path = "/etc/sepp/upp.config"</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> sepp.config.set_main_config_path(upp_config_path)</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> parser = sepp.config.get_parser()</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> parser.description = (</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/sepp/-/compare/c458c31847f39900a4dae5ae07bf816d1c1f2a40...48f6e95b4f03a20631736e9711ef824433deaf00#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">@@ -23,20 +23,60 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> mkdir -p tools/bundled/Linux</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> mkdir -p tools/merge/lib</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> # Building the jars for sepp first, tipp then.</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> cd tools/merge && \</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> CLASSPATH=/usr/share/java/jenkins-json-lib.jar:/usr/share/java/gson.jar ant</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> dh_auto_configure</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> CLASSPATH=/usr/share/java/jenkins-json-lib.jar:/usr/share/java/gson.jar ant && \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> CLASSPATH=/usr/share/java/jenkins-json-lib.jar:/usr/share/java/gson.jar ant -f tipp.xml</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> # dh_auto_configure only calls the config for sepp, we need it for tipp and</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> # upp as well.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> pybuild --configure --configure-args "tipp upp"</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> # Preparing a conffile with Debian paths for sepp.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> sed 's,path=.*\(pplacer\)$$,path=/usr/bin/\1,' `find . -name main.config` | \</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> sed 's,path=.*\(hmm[a-z]*\)$$,path=/usr/bin/\1,' | \</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> sed 's,path=.*\(seppJsonMerger.jar\)$$,path=/usr/share/sepp/\1,' > main.config</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> # Preparing a conffile with Debian paths for tipp.</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> sed 's,path=.*\(pplacer\)$$,path=/usr/bin/\1,' `find . -name tipp.config` | \</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> sed 's,path=.*\(hmm[a-z]*\)$$,path=/usr/bin/\1,' | \</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> sed 's,path=.*\(tippJsonMerger.jar\)$$,path=/usr/share/sepp/\1,' > tipp.config</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> # Preparing a conffile with Debian paths for upp.</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> sed 's,path=.*\(pplacer\)$$,path=/usr/bin/\1,' `find . -name upp.config` | \</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> sed 's,path=.*\(hmm[a-z]*\)$$,path=/usr/bin/\1,' | \</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> sed 's,path=.*\(seppJsonMerger.jar\)$$,path=/usr/share/sepp/\1,' > upp.config</span>
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29
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"></span>
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30
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">override_dh_auto_clean:</span>
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31
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> dh_auto_clean</span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> rm -rf tools/bundled</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> $(RM) -rf tools/bundled</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> $(RM) -rf tools/merge/build</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> $(RM) main.config tipp.config upp.config</span>
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33
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"></span>
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34
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">override_dh_auto_install:</span>
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35
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> dh_auto_install</span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> rm debian/sepp/usr/home.path</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> # Deleting upstream configuration file, which we are not packaging.</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> $(RM) debian/sepp/usr/home.path</span>
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37
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">#override_dh_auto_test:</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"># do_stuff_for_testing</span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">#endif</span></pre>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"># To test, we move the test tree into a subdir of /tmp and we proceed to the</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"># following changes:</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"># - change paths of configuration files from /etc to build tree;</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"># - change path of jar in /usr/share to build tree;</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"># - adapt relative path of jar to its correct place in build tree.</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">override_dh_auto_test:</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> ORIGIN_FOLDER=`pwd` && \</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> TEST_FOLDER=`mktemp -d` && \</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> cp -r test/ $$TEST_FOLDER && \</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> cd $$TEST_FOLDER && \</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> mkdir sepp/ && \</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> for F in $$(ls $$ORIGIN_FOLDER/sepp/*.py); do \</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> sed "s,/etc/sepp,$$TEST_FOLDER," $$F > sepp/$${F##*/}; \</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> done && \</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> for F in $$(ls $$ORIGIN_FOLDER/*.config); do \</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> sed "s,/usr/share/sepp,$$ORIGIN_FOLDER/tools/merge," $$F > $${F##*/}; \</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> done && \</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> cd test/unittest/ && \</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> sed "s,\".*\.jar\",\"$$ORIGIN_FOLDER/tools/merge/seppJsonMerger.jar\"," testMerge.py > testMergeCp.py && \</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> mv testMergeCp.py testMerge.py && \</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> PYTHONPATH=$$PYTHONPATH:../../ python3.8 -m unittest discover -v</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">endif</span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/compare/c458c31847f39900a4dae5ae07bf816d1c1f2a40...48f6e95b4f03a20631736e9711ef824433deaf00#9979085cf4bd85f96bf1690f49b7194102a233f0"><strong>debian/sepp.lintian-overrides</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">: </span>script-with-language-extension usr/bin/*.py</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">script-with-language-extension usr/bin/*.py</span></pre>
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