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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pilon">Debian Med / pilon</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pilon/commit/44b4e37e3c95e36707c8f26d1b788d1c0870b409">44b4e37e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-02T07:34:30Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix build (thanks to Markus Koschany)
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<strong><a href="https://salsa.debian.org/med-team/pilon/commit/ee45a7e70eeaa0048188eded5e8915c4c00e99b8">ee45a7e7</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-08-02T07:41:05Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install JAR and wrapper script, conflict with pilon-non-free
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<h4>4 changed files:</h4>
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<a href="#c6dee1d81bc8dba7c2736505de7ffe7dfdc269fa">
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+
debian/bin/pilon
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
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+
debian/install
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="c6dee1d81bc8dba7c2736505de7ffe7dfdc269fa">
<a href="https://salsa.debian.org/med-team/pilon/compare/7159319ad3831c33d12c4f59558ad6583017022a...ee45a7e70eeaa0048188eded5e8915c4c00e99b8#c6dee1d81bc8dba7c2736505de7ffe7dfdc269fa"><strong>debian/bin/pilon</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># export JAVA_HOME=/usr/lib/jvm/default-java</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">JAVA_CMD</span><span class="o" style="font-weight: 600;">=</span>java</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Include the wrappers utility script</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">.</span> /usr/lib/java-wrappers/java-wrappers.sh</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell">run_java <span class="nt" style="color: navy;">-Xms128M</span> <span class="nt" style="color: navy;">-Xmx1G</span> <span class="nt" style="color: navy;">-jar</span> /usr/share/java/pilon.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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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/pilon/compare/7159319ad3831c33d12c4f59558ad6583017022a...ee45a7e70eeaa0048188eded5e8915c4c00e99b8#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</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">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> scala,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> lib<span class="idiff left right">scala-pickling</span>-java</span>
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<td class="diff-line-num new new_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"> lib<span class="idiff left right">htsjdk</span>-java</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Standards-Version: 4.1.4</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pilon</span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pilon.git</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
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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">@@ -15,6 +15,8 @@ Package: pilon</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Depends: ${misc:Depends},</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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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> libhtsjdk-java</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Conflicts: pilon-non-free</span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Replaces: pilon-non-free</span>
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18
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Description: automated genome assembly improvement and variant detection tool</span>
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<td class="diff-line-num old_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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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> Pilon is a software tool which can be used to:</span>
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20
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> * Automatically improve draft assemblies</span>
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<li id="68d8c5c6babbf5cf109b2584c454449dbff75772">
<a href="https://salsa.debian.org/med-team/pilon/compare/7159319ad3831c33d12c4f59558ad6583017022a...ee45a7e70eeaa0048188eded5e8915c4c00e99b8#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">pilon*.jar usr/share/java</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/bin usr</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/pilon/compare/7159319ad3831c33d12c4f59558ad6583017022a...ee45a7e70eeaa0048188eded5e8915c4c00e99b8#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,3 +5,6 @@ export LC_ALL=C.UTF-8</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh $@</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">override_dh_auto_build:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> scalac -classpath /usr/share/java/htsjdk.jar -d pilon.jar src/main/scala/org/broadinstitute/pilon/*</span></pre>
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