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<h3>
Pierre Gruet 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/2e4fdc5f764b61f3916cf130cd412f70738559db">2e4fdc5f</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-06T21:35:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Keeping the etc folder in the jars
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/-/commit/08f28709497486fdac2a20888c03dee919d95dfc">08f28709</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-06T21:39:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixing insecure uri and trailing whitespaces in debian/control
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/-/commit/56101fc20065bb1465c484c93a2eac0d5f34f692">56101fc2</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-06T22:41:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replacing symlinks to jars with upstream-provided scripts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/-/commit/d6a8bdc7de8ff0a1a0eb0c11229019104e2837e7">d6a8bdc7</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-06T22:42:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapting the provided launchers scripts to Debian systems
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/-/commit/3699617e9b6c4cfae8f83b725e25489e949690d9">3699617e</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-06T22:43:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating and completing manpages of act and dnaplotter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/-/commit/57794f7c27a5dca484aa4449b7f2a79d2678627c">57794f7c</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-06T22:44:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#92000686a8bfcf22560c8fe819eeee2030f576e9">
debian/artemis.install
</a>
</li>
<li class="file-stats">
<a href="#0f79f8b65f8e3c28546c3d9b3b5101d40e3ebd45">
<span class="deleted-file">
−
debian/artemis.links
</span>
</a>
</li>
<li class="file-stats">
<a href="#16713b6f650019429c9698c95815ccf79c8cf9f4">
<span class="deleted-file">
−
debian/bin/bamview
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#2c86b708643cd7246589685e68939356ca274630">
debian/man/act.1
</a>
</li>
<li class="file-stats">
<a href="#84f70e0bec56d43a6ea08d83edd1fd770c4daf6a">
debian/man/dnaplotter.1
</a>
</li>
<li class="file-stats">
<a href="#79008705e3f8eca0d134ef96cd41d3ab55fcb6c6">
<span class="new-file">
+
debian/patches/debianize_launcher_scripts.patch
</span>
</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/ec37a5701494bb48a6f2c1965c730458a7679a6a...57794f7c27a5dca484aa4449b7f2a79d2678627c#92000686a8bfcf22560c8fe819eeee2030f576e9"><strong>debian/artemis.install</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">@@ -3,4 +3,7 @@ target/modifiedJars/act.jar usr/share/java/</td>
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3
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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="php"><span class="nx">target</span><span class="o" style="font-weight: 600;">/</span><span class="nx">modifiedJars</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bamview</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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<td class="diff-line-num new_line" data-linenumber="4" 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="LC4" class="line" lang="php"><span class="nx">target</span><span class="o" style="font-weight: 600;">/</span><span class="nx">modifiedJars</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>
</pre>
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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="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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<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="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span> <span class="nx">usr</span></span></pre>
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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="php"><span class="nx">act</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"><span class="nx">art</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></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="php"><span class="nx">bamview</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="php"><span class="nx">dnaplotter</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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<li id="0f79f8b65f8e3c28546c3d9b3b5101d40e3ebd45">
<a href="https://salsa.debian.org/med-team/artemis/-/compare/ec37a5701494bb48a6f2c1965c730458a7679a6a...57794f7c27a5dca484aa4449b7f2a79d2678627c#0f79f8b65f8e3c28546c3d9b3b5101d40e3ebd45"><strong>debian/artemis.links</strong>
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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></pre>
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<li id="16713b6f650019429c9698c95815ccf79c8cf9f4">
<a href="https://salsa.debian.org/med-team/artemis/-/compare/ec37a5701494bb48a6f2c1965c730458a7679a6a...57794f7c27a5dca484aa4449b7f2a79d2678627c#16713b6f650019429c9698c95815ccf79c8cf9f4"><strong>debian/bin/bamview</strong>
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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 -e</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC3" 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="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">JAVA_CMD</span><span class="o" style="font-weight: 600;">=</span>java</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">jarname</span><span class="o" style="font-weight: 600;">=</span>/usr/share/java/<span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span>.jar</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Include the wrappers utility script</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">.</span> /usr/lib/java-wrappers/java-wrappers.sh</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell">run_java <span class="nt" style="color: #000080;">-jar</span> <span class="nv" style="color: #008080;">$jarname</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/artemis/-/compare/ec37a5701494bb48a6f2c1965c730458a7679a6a...57794f7c27a5dca484aa4449b7f2a79d2678627c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -21,8 +21,11 @@ artemis (18.1.0+dfsg-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> * Updating dependencies as Maven now replaces ant for the build</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> * Updating debian/copyright as paths have changed</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> * Building with Maven instead of ant</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> * Fixing insecure uri and trailing whitespaces in debian/control</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> * Replacing symlinks to jars with upstream-provided scripts</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> * Updating and completing manpages of act and dnaplotter</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> Sun, 06 Sep 2020 <span class="idiff left right">15:24:5</span>6 +0200</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> Sun, 06 Sep 2020 <span class="idiff left right">22:43:1</span>6 +0200</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">artemis (17.0.1+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/artemis/-/compare/ec37a5701494bb48a6f2c1965c730458a7679a6a...57794f7c27a5dca484aa4449b7f2a79d2678627c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,7 +37,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/artemis</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/artemis.git</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">Homepage: http<span class="idiff left right">://www.sanger.ac.uk/science/tools</span>/artemis</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Homepage: http<span class="idiff left right">s://www.sanger.ac.uk/science/tool</span>/artemis</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Package: artemis</span>
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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">@@ -64,7 +64,7 @@ Depends: ${misc:Depends},</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">Description: genome browser and annotation tool</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> Artemis is a genome browser and annotation tool that allows visualisation of</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> sequence features, next generation data and the results of analyses within the</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> context of the sequence, and also its six-frame translation.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> context of the sequence, and also its six-frame translation.</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> This package includes the Artemis genome browser, the Artemis Comparison</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> Tool (ACT), and the DNAplotter and BamView utilities.</span></pre>
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<li id="2c86b708643cd7246589685e68939356ca274630">
<a href="https://salsa.debian.org/med-team/artemis/-/compare/ec37a5701494bb48a6f2c1965c730458a7679a6a...57794f7c27a5dca484aa4449b7f2a79d2678627c#2c86b708643cd7246589685e68939356ca274630"><strong>debian/man/act.1</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH ACT 1 "<span class="idiff left right">October 2015</span>"</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH ACT 1 "<span class="idiff left right">September 2020</span>"</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">act \- Artemis comparison tool for genome sequences</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B act</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.RI [ options ]</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.I SEQUENCE_1</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.I COMPARISON_1_2</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.I SEQUENCE_2</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.I ...</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> SEQUENCE An EMBL, GenBank, FASTA, or GFF3 file</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> FEATURE An Artemis TAB file, or GFF file</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> COMPARISON A BLAST comparison file in tabular format</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> -options FILE Read a text file of options from FILE</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> -chado Connect to a Chado database (using PGHOST, PGPORT, PGDATABASE, PGUSER environment variables)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> -Dblack_belt_mode=? Keep warning messages to a minimum [true,false]</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> -DuserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> -DloguserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots, take log(data)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> -DbamX=FILE[,FILE2,...] For sequence 'X' open one or more BAM, CRAM, VCF, or BCF files</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> -Dchado="h:p/d?u" Get ACT to open this CHADO database</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> -Dread_only Open CHADO database read-only</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.SH EXAMPLES</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> % act</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> % act af063097.embl af063097_v_b132222.crunch b132222.embl</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> % act -Dblack_belt_mode=true -Dbam1=MAL_0h.bam -Dbam2=MAL_7h.bam,var.raw.new.bcf</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> % act -Duserplot2=/pathToFile/userPlot</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">.SH SEE ALSO</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">.BR art (1),</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">.BR dnaplotter (1)</span></pre>
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<a href="https://salsa.debian.org/med-team/artemis/-/compare/ec37a5701494bb48a6f2c1965c730458a7679a6a...57794f7c27a5dca484aa4449b7f2a79d2678627c#84f70e0bec56d43a6ea08d83edd1fd770c4daf6a"><strong>debian/man/dnaplotter.1</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH DNAPLOTTER 1 "<span class="idiff left right">October 2015</span>"</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH DNAPLOTTER 1 "<span class="idiff left right">September 2020</span>"</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">dnaplotter \- make circular plots of genomes</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B dnaplotter</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.RI [ options ]</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">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -t FILE Read a template file</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.SH EXAMPLES</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> % dnaplotter</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> % dnaplotter -t <template-file></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">.SH SEE ALSO</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> http://www.sanger.ac.uk/science/tools/dnaplotter/</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">.BR art (1),</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">.BR act (1)</span></pre>
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<li id="79008705e3f8eca0d134ef96cd41d3ab55fcb6c6">
<a href="https://salsa.debian.org/med-team/artemis/-/compare/ec37a5701494bb48a6f2c1965c730458a7679a6a...57794f7c27a5dca484aa4449b7f2a79d2678627c#79008705e3f8eca0d134ef96cd41d3ab55fcb6c6"><strong>debian/patches/debianize_launcher_scripts.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Simplifying the provided launchers</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Many options or tricks are useless on a Debian system.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> The paths are also adapted to the Debian install.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2020-09-06</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">--- a/act</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/act</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -38,36 +38,6 @@</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> exit 0</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> }</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_proxy_properties() {</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [[ "$http_proxy" = "" ]]</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- http_proxy=$HTTP_PROXY</span></span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [[ "$http_proxy" = "" ]]</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- http_proxy=$HTTP_proxy</span></span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [[ "$http_proxy" != "" ]]</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Resolve script path (inc symlinks)</span></span>
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34
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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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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-SOURCE="${BASH_SOURCE[0]}"</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SOURCE="$(readlink "$SOURCE")"</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-done</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" 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="LC44" class="line" lang="diff"> # Special Sanger override on chado PGUSER</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> then</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -93,28 +63,6 @@</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> shift</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> done</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JAR_NAME=act.jar</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Use a custom Java version if necessary</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-then</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAVA=`which java`</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAVA_HOME=$ARTEMIS_JAVA_JRE</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAVA=$ARTEMIS_JAVA_JRE/bin/java</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Allow URLs to work from behind firewalls.</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_proxy_properties</span></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;">-</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> #</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> # "-mx2g" sets the maximum amount of memory to use. </span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> # This may need to be increased when dealing with large files</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="p">@@ -132,20 +80,12 @@</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> #</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> </span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PLATTMP=`uname`</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [[ "$PLATTMP" = "Darwin" ]]</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=ACT"</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;">- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> if [[ "$QUIET" = no ]]</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> then</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> echo "Starting ACT with arguments: $FLAGS $APPLICATION_PROPERTIES $*"</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> fi</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.ActMain $*</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/java/act.jar $*</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> result=$?</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> </span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> exit $result</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/art</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/art</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="p">@@ -44,36 +44,6 @@</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> exit 0</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_proxy_properties() {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [[ "$http_proxy" = "" ]]</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- http_proxy=$HTTP_PROXY</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [[ "$http_proxy" = "" ]]</span></span>
</pre>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- http_proxy=$HTTP_proxy</span></span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [[ "$http_proxy" != "" ]]</span></span>
</pre>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`</span></span>
</pre>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
</pre>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
</pre>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="123" 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">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Resolve script path (inc symlinks)</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-SOURCE="${BASH_SOURCE[0]}"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SOURCE="$(readlink "$SOURCE")"</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-done</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> # Special Sanger override on chado PGUSER</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> then</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="p">@@ -99,28 +69,6 @@</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> shift</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> done</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> </span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JAR_NAME=artemis.jar</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Use a custom Java version if necessary</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-then</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAVA=`which java`</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAVA_HOME=$ARTEMIS_JAVA_JRE</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAVA=$ARTEMIS_JAVA_JRE/bin/java</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Allow URLs to work from behind firewalls.</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_proxy_properties</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> #</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> # "-mx2g" sets the maximum amount of memory to use. </span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> # This may need to be increased when dealing with large files</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="p">@@ -139,20 +87,12 @@</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> #</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> </span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PLATTMP=`uname`</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [[ "$PLATTMP" = "Darwin" ]]</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-then</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=Artemis"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> if [[ "$QUIET" = "no" ]]</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> then</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> echo "Starting Artemis with arguments: $FLAGS $APPLICATION_PROPERTIES $*"</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> fi</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.ArtemisMain $*</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/java/artemis.jar $*</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> result=$?</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> </span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> exit $result</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bamview</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bamview</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="p">@@ -6,57 +6,7 @@</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> </span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> QUIET=no</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> </span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_proxy_properties() {</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [[ "$http_proxy" = "" ]]</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- http_proxy=$HTTP_PROXY</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [[ "$http_proxy" = "" ]]</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- http_proxy=$HTTP_proxy</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [[ "$http_proxy" != "" ]]</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" 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">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Resolve script path (inc symlinks)</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-SOURCE="${BASH_SOURCE[0]}"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink</span></span>
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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SOURCE="$(readlink "$SOURCE")"</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-done</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JAR_NAME=bamview.jar</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Use a custom Java version if necessary</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-then</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAVA=`which java`</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAVA_HOME=$ARTEMIS_JAVA_JRE</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAVA=$ARTEMIS_JAVA_JRE/bin/java</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Allow URLs to work from behind firewalls.</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_proxy_properties</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> </span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> #</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> # "-mx2g" sets the maximum amount of memory to use. </span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="p">@@ -69,20 +19,12 @@</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> FLAGS="$ARTEMIS_JVM_FLAGS -noverify"</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> fi</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> </span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PLATTMP=`uname`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="253" 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">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [[ "$PLATTMP" = "Darwin" ]]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-then</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Xdock:name=BamView"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="258" 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">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> if [[ "$QUIET" = "no" ]]</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> then</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> fi</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.alignment.BamView $*</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/java/bamview.jar $*</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> result=$?</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> </span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> exit $result</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/dnaplotter</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/dnaplotter</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="p">@@ -25,37 +25,6 @@</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> exit 0</span>
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<td class="diff-line-num new new_line" data-linenumber="274" 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">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> }</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> </span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_proxy_properties() {</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [[ "$http_proxy" = "" ]]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" 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">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- http_proxy=$HTTP_PROXY</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [[ "$http_proxy" = "" ]]</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- http_proxy=$HTTP_proxy</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [[ "$http_proxy" != "" ]]</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- then</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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<td class="diff-line-num new new_line" data-linenumber="296" 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">
296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Resolve script path (inc symlinks)</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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<td class="diff-line-num new new_line" data-linenumber="298" 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">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-SOURCE="${BASH_SOURCE[0]}"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SOURCE="$(readlink "$SOURCE")"</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-done</span></span>
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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> #</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> # Parse arguments.</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> #</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="p">@@ -75,28 +44,6 @@</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> shift</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> done</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> </span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="315" 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">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JAR_NAME=dnaplotter.jar</span></span>
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<td class="diff-line-num new new_line" data-linenumber="316" 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">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME</span></span>
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<td class="diff-line-num new new_line" data-linenumber="318" 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">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Use a custom Java version if necessary</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-then</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAVA=`which java`</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAVA_HOME=$ARTEMIS_JAVA_JRE</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAVA=$ARTEMIS_JAVA_JRE/bin/java</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Allow URLs to work from behind firewalls.</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_proxy_properties</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" 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="LC336" class="line" lang="diff"> #</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> # "-mx2g" sets the maximum amount of memory to use. </span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> # This may need to be increased when dealing with large files</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="p">@@ -108,20 +55,12 @@</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> FLAGS="$ARTEMIS_JVM_FLAGS -noverify"</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> fi</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> </span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PLATTMP=`uname`</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [[ "$PLATTMP" = "Darwin" ]]</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-then</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=Circular-Plot"</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-fi</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> if [[ "$QUIET" = "no" ]]</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> then</span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> fi</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> </span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/java/dnaplotter.jar $TEMPLATE_FILE_ARG</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> result=$?</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> exit $result</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/artemis/-/compare/ec37a5701494bb48a6f2c1965c730458a7679a6a...57794f7c27a5dca484aa4449b7f2a79d2678627c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" 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">@@ -4,3 +4,4 @@ using_system_jars_in_pom.patch</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">missing_htsjdk_dependency_in_pom.patch</span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">no_install_of_provided_jars.patch</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">running_build_tests.patch</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">debianize_launcher_scripts.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/artemis/-/compare/ec37a5701494bb48a6f2c1965c730458a7679a6a...57794f7c27a5dca484aa4449b7f2a79d2678627c#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">@@ -40,7 +40,7 @@ override_dh_auto_build:</td>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> # but we don't use it since it creates shaded jars.</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> cd target/ && mkdir jarsBuild && mkdir modifiedJars && cd jarsBuild && \</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> jar xf ../artemis-*.jar && \</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> $(RM) -rf <span class="idiff left right">etc/ </span>META_INF/ && \</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> $(RM) -rf META_INF/ && \</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> jar cf artemis.jar * && \</span>
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<td class="diff-line-num old_line" data-linenumber="45" 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="LC45" class="line" lang="plaintext"> mv artemis.jar ../modifiedJars/ && \</span>
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<td class="diff-line-num old_line" data-linenumber="46" 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="diff-line-num new_line" data-linenumber="46" 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="LC46" class="line" lang="plaintext"> cp ../modifiedJars/artemis.jar ../modifiedJars/act.jar && \</span>
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