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<h3>
Olivier Sallou pushed to branch master
at <a href="https://salsa.debian.org/med-team/picard-tools">Debian Med / picard-tools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/0724ae2755332b527df4d35a24b40c3982bad007">0724ae27</a></strong>
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<span>by Olivier Sallou</span>
<i>at 2019-01-17T17:48:30Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix manifest for runtime deps closes #919559
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/c93e1866f9549e899c8ce00549e94bd3b53f1804">c93e1866</a></strong>
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<span>by Olivier Sallou</span>
<i>at 2019-01-17T17:48:30Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set current investigation status
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#4ac01070feee0f0c017d8fa6afa466b49a18888f">
debian/bin/PicardCommandLine
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#07cf65e813f1d838319cc6f62fd4cd773646e99e">
<span class="new-file">
+
debian/libpicard-java.manifest
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<h4>Changes:</h4>
<li id="4ac01070feee0f0c017d8fa6afa466b49a18888f">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/077712af88da3e0f85fb1c3949b7c468b895577a...c93e1866f9549e899c8ce00549e94bd3b53f1804#4ac01070feee0f0c017d8fa6afa466b49a18888f"><strong>debian/bin/PicardCommandLine</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">@@ -12,4 +12,6 @@ PicardCommandLine)</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">esac</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">USE_LIBRARY_PATH</span><span class="o" style="font-weight: 600;">=</span>USE_LIBRARY_PATH</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exec </span>java <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">JAVA_OPTIONS</span><span class="p">-</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: navy;">-jar</span> /usr/share/java/picard.jar <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">PICARD_CLASSPATH</span><span class="o" style="font-weight: 600;">=</span>/usr/share/java/picard.jar:/usr/share/java/htsjdk.jar:/usr/share/java/guava.jar:/usr/lib/jvm/default-java/lib/tools.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/gkl.jar:/usr/share/java/gatk-native-bindings.jar:/usr/share/java/barclay.jar</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exec </span>java <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">JAVA_OPTIONS</span><span class="p">-</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: navy;">-cp</span> <span class="nv" style="color: teal;">$PICARD_CLASSPATH</span> picard.cmdline.PicardCommandLine <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/077712af88da3e0f85fb1c3949b7c468b895577a...c93e1866f9549e899c8ce00549e94bd3b53f1804#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">picard-tools (2.18.23+dfsg-2) UNRELEASE; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Fix Class-Path in manifest file for dependencies (Closes: #919559).</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> [TODO] 2 tests are still failing with autopkgtest though source build</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> and testing works fine.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Olivier Sallou <osallou@debian.org> Thu, 17 Jan 2019 15:54:27 +0000</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">picard-tools (2.18.23+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * New upstream version</span>
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<li id="07cf65e813f1d838319cc6f62fd4cd773646e99e">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/077712af88da3e0f85fb1c3949b7c468b895577a...c93e1866f9549e899c8ce00549e94bd3b53f1804#07cf65e813f1d838319cc6f62fd4cd773646e99e"><strong>debian/libpicard-java.manifest</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/java/picard.jar:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Main-Class: picard.cmdline.PicardCommandLine</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Class-Path: /usr/share/java/htsjdk.jar:/usr/share/java/guava.jar:/usr/lib/jvm/default-java/lib/tools.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/gkl.jar:/usr/share/java/gatk-native-bindings.jar:/usr/share/java/barclay.jar</span></pre>
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