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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/artemis">Debian Med / artemis</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/commit/b6834336f23b25cafcbcef1ccd66ff63f0b858da">b6834336</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-05T15:36:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Restricted set of tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/commit/35bedc44b0e44b8dd79b01a8f20dcc3a2f4cfeef">35bedc44</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-06T07:56:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix names, fix patch
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#92000686a8bfcf22560c8fe819eeee2030f576e9">
debian/artemis.install
</a>
</li>
<li class="file-stats">
<a href="#0f79f8b65f8e3c28546c3d9b3b5101d40e3ebd45">
debian/artemis.links
</a>
</li>
<li class="file-stats">
<a href="#9fda2c589fa8d24b403731e01af05723bea25b24">
debian/artemis.manifest.in
</a>
</li>
<li class="file-stats">
<a href="#d868ab7f769125e66a23484c0b2cd648eeaff096">
debian/patches/jar-rules.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="92000686a8bfcf22560c8fe819eeee2030f576e9">
<a href="https://salsa.debian.org/med-team/artemis/compare/551ab850a0023d1cc4ffba2839d2b3fe3b21dbe8...35bedc44b0e44b8dd79b01a8f20dcc3a2f4cfeef#92000686a8bfcf22560c8fe819eeee2030f576e9"><strong>debian/artemis.install</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="nx">jar_build</span><span class="o" style="font-weight: 600;">/</span><span class="nx">artemis</span><span class="o" style="font-weight: 600;">.</span><span class="nx">jar</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">java</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="nx">jar_build</span><span class="o" style="font-weight: 600;">/</span><span class="nx">act</span><span class="o" style="font-weight: 600;">.</span><span class="nx">jar</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">java</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="php"><span class="nx">jar_build</span><span class="o" style="font-weight: 600;">/</span><span class="nx"><span class="idiff left right">BamV</span>iew</span><span class="o" style="font-weight: 600;">.</span><span class="nx">jar</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">java</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="nx">jar_build</span><span class="o" style="font-weight: 600;">/</span><span class="nx"><span class="idiff left right">bamv</span>iew</span><span class="o" style="font-weight: 600;">.</span><span class="nx">jar</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">java</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="nx">jar_build</span><span class="o" style="font-weight: 600;">/</span><span class="nx">DNAPlotter</span><span class="o" style="font-weight: 600;">.</span><span class="nx">jar</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">java</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">desktop</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">desktop</span> <span class="idiff left right"> </span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">applications</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">desktop</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">desktop</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">applications</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="php"><span class="nx">images</span><span class="o" style="font-weight: 600;">/</span><span class="nx">helix</span><span class="o" style="font-weight: 600;">.</span><span class="nx">png</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">icons</span><span class="o" style="font-weight: 600;">/</span><span class="nx">hicolor</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">96</span><span class="nx">x96</span><span class="o" style="font-weight: 600;">/</span><span class="nx">apps</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<li id="0f79f8b65f8e3c28546c3d9b3b5101d40e3ebd45">
<a href="https://salsa.debian.org/med-team/artemis/compare/551ab850a0023d1cc4ffba2839d2b3fe3b21dbe8...35bedc44b0e44b8dd79b01a8f20dcc3a2f4cfeef#0f79f8b65f8e3c28546c3d9b3b5101d40e3ebd45"><strong>debian/artemis.links</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">usr/share/java/artemis.jar usr/bin/art</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">usr/share/java/act.jar usr/bin/act</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">usr/share/java/DNAPlotter.jar usr/bin/dnaplotter</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">usr/share/java/<span class="idiff left right">BamV</span>iew.jar usr/bin/bamview</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">usr/share/java/<span class="idiff left right">bamv</span>iew.jar usr/bin/bamview</span></pre>
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<li id="9fda2c589fa8d24b403731e01af05723bea25b24">
<a href="https://salsa.debian.org/med-team/artemis/compare/551ab850a0023d1cc4ffba2839d2b3fe3b21dbe8...35bedc44b0e44b8dd79b01a8f20dcc3a2f4cfeef#9fda2c589fa8d24b403731e01af05723bea25b24"><strong>debian/artemis.manifest.in</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">@@ -6,7 +6,7 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Class-Path: @CLASSPATH@</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> Main-Class: uk.ac.sanger.artemis.components.ActMain</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> Permissions: all-permissions</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">/usr/share/java/<span class="idiff left right">BamV</span>iew.jar:</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">/usr/share/java/<span class="idiff left right">bamv</span>iew.jar:</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> Class-Path: @CLASSPATH@</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> Main-Class: uk.ac.sanger.artemis.components.alignment.BamView</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> Permissions: all-permissions</span>
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<a href="https://salsa.debian.org/med-team/artemis/compare/551ab850a0023d1cc4ffba2839d2b3fe3b21dbe8...35bedc44b0e44b8dd79b01a8f20dcc3a2f4cfeef#d868ab7f769125e66a23484c0b2cd648eeaff096"><strong>debian/patches/jar-rules.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">@@ -50,7 +50,7 @@ Last-Update: Sun, 05 Aug 2018 07:16:40 +0200</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw\nPermissions: all-permissions" > manifest-circular; \</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> jar cmf manifest-circular ../DNAPlotter.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg README.md etc \</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;">- org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ org uk <span class="idiff left right">joptsimple ngs freemarker </span>; \</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ org uk ; \</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView\nPermissions: all-permissions" > manifest-bamview; \</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;">- jar cmf manifest-bamview ../bamview.jar META-INF/services etc org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE; \</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;">+ jar cmf manifest-bamview ../bamview.jar etc org uk ; \</span></span>
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<a href="https://salsa.debian.org/med-team/artemis/compare/551ab850a0023d1cc4ffba2839d2b3fe3b21dbe8...35bedc44b0e44b8dd79b01a8f20dcc3a2f4cfeef#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">@@ -3,3 +3,4 @@ jar-rules.patch</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">test-classpath.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">samreader.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">use-lang3.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">fix-test.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/artemis/compare/551ab850a0023d1cc4ffba2839d2b3fe3b21dbe8...35bedc44b0e44b8dd79b01a8f20dcc3a2f4cfeef#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">@@ -44,7 +44,7 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> convert images/helix.gif -resize 96x96\! images/helix.png</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> cd test && ant -f build-test.xml -DEMBOSS_ROOT=/usr</span>
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<td class="diff-line-num new old_line" data-linenumber="48" 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="LC47" class="line" lang="plaintext"> cd test && ant -f build-test.xml <span class="idiff left right">run-manual-tests-headless </span>-DEMBOSS_ROOT=/usr</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> dh_auto_clean</span>
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