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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/4d21ab120282b5a64f3f9b49da67bc02eb720d53">4d21ab12</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-06T14:46:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Setting the classpath in d/rules is not needed with a Maven build
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/-/commit/241e417127b00b8355908a6befdfa717a9ff205f">241e4171</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-06T15:25:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">with-javahelper -> with javahelper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/-/commit/25d15bd3b933438fed66a1a198c96f0df2b890bb">25d15bd3</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-06T15:29:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/-/commit/d129dbb90167efe7629df701d4f8685eee1ab39e">d129dbb9</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-06T20:18:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#331b1c060f8aeee7b584650fecb9d0d109fda290">
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+
debian/artemis.manifest
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<a href="#9fda2c589fa8d24b403731e01af05723bea25b24">
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−
debian/artemis.manifest.in
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="331b1c060f8aeee7b584650fecb9d0d109fda290">
<a href="https://salsa.debian.org/med-team/artemis/-/compare/7075fb82dd3e5873024d27244ad15c74cfc876d1...d129dbb90167efe7629df701d4f8685eee1ab39e#331b1c060f8aeee7b584650fecb9d0d109fda290"><strong>debian/artemis.manifest</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/java/artemis.jar:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/batik-codec.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar /usr/share/java/biojava.jar /usr/share/java/cglib.jar /usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar /usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar /usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar /usr/share/java/postgresql-jdbc.jar</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Main-Class: uk.ac.sanger.artemis.components.ArtemisMain</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">usr/share/java/act.jar:</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar /usr/share/java/biojava.jar /usr/share/java/cglib.jar /usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar /usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar /usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar /usr/share/java/postgresql-jdbc.jar</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Main-Class: uk.ac.sanger.artemis.components.ActMain</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">usr/share/java/bamview.jar:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar /usr/share/java/biojava.jar /usr/share/java/cglib.jar /usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar /usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar /usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar /usr/share/java/postgresql-jdbc.jar</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> Main-Class: uk.ac.sanger.artemis.components.alignment.BamView</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">usr/share/java/dnaplotter.jar:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Class-Path: /usr/share/java/artemis.jar /usr/share/java/batik-codec.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar /usr/share/java/biojava.jar /usr/share/java/cglib.jar /usr/share/java/commons-lang3.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-net.jar /usr/share/java/htsjdk.jar /usr/share/java/ibatis.jar /usr/share/java/j2ssh-core.jar /usr/share/java/log4j-1.2.jar /usr/share/java/picard.jar /usr/share/java/postgresql-jdbc.jar</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Main-Class: uk.ac.sanger.artemis.circular.DNADraw</span></pre>
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<li id="9fda2c589fa8d24b403731e01af05723bea25b24">
<a href="https://salsa.debian.org/med-team/artemis/-/compare/7075fb82dd3e5873024d27244ad15c74cfc876d1...d129dbb90167efe7629df701d4f8685eee1ab39e#9fda2c589fa8d24b403731e01af05723bea25b24"><strong>debian/artemis.manifest.in</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">/usr/share/java/artemis.jar:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Class-Path: @CLASSPATH@</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Main-Class: uk.ac.sanger.artemis.components.ArtemisMain</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Permissions: all-permissions</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">/usr/share/java/act.jar:</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Class-Path: @CLASSPATH@</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Main-Class: uk.ac.sanger.artemis.components.ActMain</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Permissions: all-permissions</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">/usr/share/java/bamview.jar:</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> Class-Path: @CLASSPATH@</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> Main-Class: uk.ac.sanger.artemis.components.alignment.BamView</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> Permissions: all-permissions</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">/usr/share/java/dnaplotter.jar:</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> Class-Path: @CLASSPATH@</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> Main-Class: uk.ac.sanger.artemis.circular.DNADraw</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> Permissions: all-permissions</span></pre>
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<a href="https://salsa.debian.org/med-team/artemis/-/compare/7075fb82dd3e5873024d27244ad15c74cfc876d1...d129dbb90167efe7629df701d4f8685eee1ab39e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">artemis (18.1.0+dfsg-5) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Upload to unstable, setting the package as Architecture: all seems to be</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> OK in experimental</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Setting the classpath in d/rules is not needed with a Maven build</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Pierre Gruet <pgt@debian.org> Sat, 06 Nov 2021 15:29:24 +0100</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">artemis (18.1.0+dfsg-4) experimental; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Removing useless dependency on jarwrapper</span>
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<a href="https://salsa.debian.org/med-team/artemis/-/compare/7075fb82dd3e5873024d27244ad15c74cfc876d1...d129dbb90167efe7629df701d4f8685eee1ab39e#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">@@ -2,36 +2,8 @@</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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4
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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">JAVA_HOME=/usr/lib/jvm/default-java</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">CUPBOARD = biojava \</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> j2ssh-core \</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> ibatis \</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> log4j-1.2 \</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> postgresql-jdbc3 \</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> picard \</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> htsjdk \</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> commons-logging \</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> commons-net \</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> commons-lang3 \</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> cglib \</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> batik-codec \</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> batik-dom \</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> batik-ext \</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> batik-svggen \</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> batik-util</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"># hack to be able to use a space as an argument to the subst function</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">space=</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">space+=</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">CLASSPATH := $(foreach jar, $(CUPBOARD), /usr/share/java/$(jar).jar)</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">CLASSPATH += /usr/share/EMBOSS/jemboss/lib/jemboss.jar \</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> $(CURDIR)</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">export CLASSPATH := $(subst $(space),:,$(strip $(CLASSPATH)))</span>
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<pre style="margin: 0;">-<span id="LC32" 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">%:</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> dh $@<span class="idiff left right"> --with javahelper</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh_auto_build</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" 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">@@ -48,10 +20,6 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> jar cf dnaplotter.jar * && \</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> mv dnaplotter.jar ../modifiedJars/ && \</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> cp ../modifiedJars/dnaplotter.jar ../modifiedJars/bamview.jar</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> # Preparing the classpath for jh_manifest, which will fix the classpath and</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> # the main class.</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> sed 's|@CLASSPATH@|$(subst :,$(space),$(subst $(CURDIR),/usr/share/java/artemis.jar,$(CLASSPATH)))|g' debian/artemis.manifest.in > \</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> debian/artemis.manifest</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="29" 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">@@ -61,7 +29,6 @@ endif</td>
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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">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> $(RM) debian/artemis.manifest</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> $(RM) images/helix.png</span>
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66
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> $(RM) -rf target/jarsBuild</span>
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67
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> $(RM) -rf target/modifiedJars</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,5 +38,3 @@ override_dh_install:</td>
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71
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> # Using imagemagick to convert the icon from gif to png.</span>
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<td class="old_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
72
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> mkdir -p debian/$(DEB_SOURCE)/usr/share/icons/hicolor/96x96/apps/</span>
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<td class="old_line diff-line-num" data-linenumber="73" 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">
73
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> convert src/main/resources/images/helix.gif -resize 96x96\! debian/$(DEB_SOURCE)/usr/share/icons/hicolor/96x96/apps/helix.png</span></pre>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> # Defining the right classpaths and main classes.</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> jh_manifest</span></pre>
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