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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/igv">Debian Med / igv</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/igv/-/commit/2d136846fa2ff65a0eee7de5027348c244db7773">2d136846</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-08-29T15:49:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Revert "Update upstream source from tag 'upstream/2.8.10+dfsg'"
This reverts commit 61632fccf2902363cc801e8e25b98b888a787087, reversing
changes made to 14c8d69031f3636747cf9885ddfe8336a11bc85a.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/igv/-/commit/dff1843810e1f6c61600431b6206c5ffce0ba580">dff18438</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-08-29T19:27:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bringing back changelog to version 2.6.3+dfsg
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/igv/-/commit/9f98cb1885db8cf4673b968968bd3ee4c84a7a60">9f98cb18</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-08-29T19:28:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Revert "No need to fiddle around with build.gradle files any more"
This reverts commit 9820402dcd69d14b3647b9c83bc2bfc850179994.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/igv/-/commit/383eb0dde24282d26a8d6d3d0398ac541a8dc2c0">383eb0dd</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-01T21:00:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating build directory to Java 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/igv/-/commit/22a30171cd3bca3473fc330a2f81294ef3d9e8c2">22a30171</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-01T21:00:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add runtime dependency to batik
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/igv/-/commit/20ac77eedd00c54751e23062a858dbe8a181dccf">20ac77ee</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-01T21:01:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapting paths for gradle as we use Debian libs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/igv/-/commit/e7c6cf9eba06012c35973c022bcba448c84fa785">e7c6cf9e</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-01T21:02:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapting the code, written for an old htsjdk version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/igv/-/commit/529655a280e2ad4da84eeb51ef3c0ba2dea4465b">529655a2</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-01T21:03:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Skipping build-time tests that require an access to network
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/igv/-/commit/263782504d1c7a122d9a329e7a0fa318367deaa0">26378250</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-01T22:19:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
</li>
<li class="file-stats">
<a href="#26faf2a07a9e1acfeeda717bc1a5b409d726f22e">
IGV.iml
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#f07866736216be0ee2aba49e392191aeae700a35">
build.gradle
</a>
</li>
<li class="file-stats">
<a href="#0ae54ab4d88e06323920d027649da7246640130f">
<span class="new-file">
+
build_java11.gradle
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#4c8d972d9b3b135eca315c9b886dfaa9d4fc4171">
debian/igv.jlibs
</a>
</li>
<li class="file-stats">
<a href="#f9271eab4da87b925b1f65845b9ce74b6c675af3">
<span class="new-file">
+
debian/patches/gradle_dependencies.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#f11af076ef5b585c32b9737349cdc89bdb5ac0a0">
<span class="new-file">
+
debian/patches/handle_old_htsjdk.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#158c9a83bf6361eb3dab802707c2ce0bb9662494">
<span class="new-file">
+
debian/patches/skip_tests_network.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#e996eb6a59ba3e1f59429a84239f9bc1158cd221">
<span class="deleted-file">
−
docs/AWS.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#0b59a06aec235c8ae40c4513f351a515b779a0c6">
genomes/db/hg19/hg19_annotations.xml
</a>
</li>
<li class="file-stats">
<a href="#06af505b8fe47918e4aa2c7640e331d75611f2cb">
genomes/db/hg19/hg19_dataServerRegistry.txt
</a>
</li>
<li class="file-stats">
<a href="#f600f684fc7097c845838671cc23117598648f06">
<span class="deleted-file">
−
genomes/db/hg19/tcga_stddata__2016_01_28.xml
</span>
</a>
</li>
<li class="file-stats">
<a href="#7869d51c2abcd300ad4d1b550c0ce78f64f7bd56">
<span class="deleted-file">
−
genomes/db/hg19/tutorials.hg19.xml
</span>
</a>
</li>
<li class="file-stats">
<a href="#79af1f1fc0b2f1f64f1360f3f80e71bb81998051">
genomes/genomes.txt
</a>
</li>
<li class="file-stats">
<a href="#ec27dae6e852c099bfcae8de5204d286bb6f04ff">
gradle/wrapper/gradle-wrapper.jar
</a>
</li>
<li class="file-stats">
<a href="#fbe448ebfc3eb2d4e308f6b8b043666f5b57235e">
gradle/wrapper/gradle-wrapper.properties
</a>
</li>
<li class="file-stats">
<a href="#5bbfa66edb4db3c7c33c5181f43510990d3307f9">
gradlew
</a>
</li>
<li class="file-stats">
<a href="#2a45a911a8f1836b0b6c5b758962572012d8f8c3">
gradlew.bat
</a>
</li>
<li class="file-stats">
<a href="#ef54b3754d35455eba7cd94a22d18ca3d3704bc9">
<span class="new-file">
+
lib/AbsoluteLayout.jar
</span>
</a>
</li>
<li class="file-stats">
<a href="#af215dda44c4f59b386cd07980871055895740b7">
<span class="new-file">
+
lib/goby-io-igv-1.1.jar
</span>
</a>
</li>
<li class="file-stats">
<a href="#ddc8cf35d1f13667df623a146674bed9127cbbfd">
<span class="new-file">
+
lib/jide-common-3.7.3.jar
</span>
</a>
</li>
<li class="file-stats">
<a href="#45bb220a63be74ec5e7aae4b40ecda611c153adb">
<span class="deleted-file">
−
scripts/igv-launcher.bat
</span>
</a>
</li>
<li class="file-stats">
<a href="#a289ffe94e4675c3650f1ce675616092e8f63afc">
scripts/igv.bat
</a>
</li>
<li class="file-stats">
<a href="#e2b3b7ad7925dd429929038ac625df473e8789fc">
scripts/igv.command
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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<p style="font-size: small; color: #777;">
—
<br>
<a href="https://salsa.debian.org/med-team/igv/-/compare/9820402dcd69d14b3647b9c83bc2bfc850179994...263782504d1c7a122d9a329e7a0fa318367deaa0">View it on GitLab</a>.
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