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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/libgoby-java">Debian Med / libgoby-java</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/aedb2043c3b9d1fd0eb36ed6e695bca71440db76">aedb2043</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-08-07T15:17:02+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Splitting the binary package into two ones, for licensing concerns
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#35ed685909bc161ac11cc911cd8f8551ea8ffc46">
<span class="new-file">
+
debian/goby-java.install
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<li class="file-stats">
<a href="#0381ec0c3b0200674f7b457844cf110b4aa8d66b">
debian/libgoby-java.manifest
→
debian/goby-java.manifest
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<li class="file-stats">
<a href="#7a8f9e9cb64b103e1817e521ca3fc40fcc7d49db">
<span class="new-file">
+
debian/libgoby-io-java.manifest
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<li class="file-stats">
<a href="#f9590ff6a2d5aa749ea2bea129dacf1fc7b0896c">
debian/libgoby-java.poms
→
debian/libgoby-io-java.poms
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</li>
<li class="file-stats">
<a href="#858bea9722a154016dfe6cf0c870a2c893749921">
<span class="deleted-file">
−
debian/libgoby-java.links
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</a>
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</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/aedb2043c3b9d1fd0eb36ed6e695bca71440db76#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="51" 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">@@ -51,15 +51,34 @@ Vcs-Git: https://salsa.debian.org/med-team/libgoby-java.git</td>
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51
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">Homepage: http://campagnelab.org/software/goby/</span>
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<td class="old_line diff-line-num" data-linenumber="52" 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="LC52" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">Package: libgoby-java</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ny</span></span>
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<td class="old_line diff-line-num new" data-linenumber="56" 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="LC54" class="line" lang="plaintext">Package: libgoby-<span class="idiff left right">io-</span>java</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ll</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> ${maven:Depends},</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> libcommons-collections3-java,</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> libdistlib-java,</span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> libjbzip2-java,</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> libpj-java,</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> libpj-java</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">Recommends: ${java:Recommends},</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> ${maven:OptionalDepends}</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">Description: IO API for goby</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> Goby is a next-gen data management framework designed to facilitate the</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> implementation of efficient data analysis pipelines.</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> Goby provides very efficient file formats to store next-generation sequencing</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> data and intermediary analysis results.</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> This package contains the Goby IO API, including code necessary to read and</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> write Goby file formats. It is released under the LGPL3 license.</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">Package: goby-java</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> ${misc:Depends},</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> ${maven:Depends},</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> default-jre,</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> libgoby-io-java (= ${binary:Version}),</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> libdistlib-java,</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> r-cran-rjava</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext">Recommends: ${java:Recommends},</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"> ${maven:OptionalDepends}</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">@@ -68,10 +87,10 @@ Description: store next-generation sequencing data and intermediary analysis res</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"> implementation of efficient data analysis pipelines.</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"> Goby provides very efficient file formats to store next-generation sequencing</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> data and intermediary analysis results. Goby 1.x files were compressed with</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> GZip. Goby 2.0 introduced novel compression approaches that result in state</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> of the art compression of alignment data. Goby 2.0 files can compress to a few</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> percent of a BAM file and are often smaller than CRAM files.</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> data and intermediary analysis results.</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"> Goby also provides utilities that implement common next-gen data computations.</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> These utilities are designed to be relatively easy to use, yet very efficient.</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> This package provides the entire Goby framework, including application</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> programs (i.e., Goby modes). It is released under the GPL3 license.</span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/aedb2043c3b9d1fd0eb36ed6e695bca71440db76#35ed685909bc161ac11cc911cd8f8551ea8ffc46"><strong>debian/goby-java.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">goby</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span></pre>
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<strong>debian/goby-java.manifest</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/share/java/goby-io.jar:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-exex.jar /usr/share/java/commons-io.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/dsiutils.jar /usr/share/java/fastutil.jar /usr/share/java/htsjdk.jar /usr/share/java/icb-utils.jar /usr/share/java/jbzip2.jar /usr/lib/R/site-library/rJava/jri/JRI.jar /usr/share/java/jsap.jar /usr/share/java/pj.jar /usr/share/java/protobuf.jar /usr/share/java/reflections.jar /usr/share/java/slf4j.jar</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">usr/share/java/goby-distribution.jar:</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-exex.jar /usr/share/java/commons-io.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/dsiutils.jar /usr/share/java/fastutil.jar /usr/share/java/goby-io.jar /usr/share/java/htsjdk.jar /usr/share/java/icb-utils.jar /usr/share/java/jbzip2.jar /usr/lib/R/site-library/rJava/jri/JRI.jar /usr/share/java/jsap.jar /usr/share/java/pj.jar /usr/share/java/protobuf.jar /usr/share/java/reflections.jar /usr/share/java/slf4j.jar /usr/share/java/distlib.jar</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> Main-Class: org.campagnelab.goby.modes.GobyDriver</span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/aedb2043c3b9d1fd0eb36ed6e695bca71440db76#7a8f9e9cb64b103e1817e521ca3fc40fcc7d49db"><strong>debian/libgoby-io-java.manifest</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/java/goby-io.jar:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-exex.jar /usr/share/java/commons-io.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/dsiutils.jar /usr/share/java/fastutil.jar /usr/share/java/htsjdk.jar /usr/share/java/icb-utils.jar /usr/share/java/jbzip2.jar /usr/share/java/jsap.jar /usr/share/java/pj.jar /usr/share/java/protobuf.jar /usr/share/java/reflections.jar /usr/share/java/slf4j.jar</span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/aedb2043c3b9d1fd0eb36ed6e695bca71440db76#f9590ff6a2d5aa749ea2bea129dacf1fc7b0896c"><strong>debian/libgoby-java.poms</strong>
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<strong>debian/libgoby-io-java.poms</strong>
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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">@@ -26,6 +26,6 @@</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"># Empty by default. [mh_install]</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">pom.xml --has-package-version</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">goby-distribution/pom.xml</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">goby-distribution/pom.xml<span class="idiff left right"> --java-lib --package=goby-java</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">goby-io/pom.xml</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">goby-spi/pom.xml --ignore</span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/aedb2043c3b9d1fd0eb36ed6e695bca71440db76#858bea9722a154016dfe6cf0c870a2c893749921"><strong>debian/libgoby-java.links</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/share/java/goby-distribution.jar usr/share/java/goby.jar</span></pre>
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