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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/strelka">Debian Med / strelka</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/strelka/-/commit/db7dcedd9656926d870a2b46b8c597e49f1a9be7">db7dcedd</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-15T14:19:26+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TODO: Prevent cmake from checking whether install can write to /usr
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<h4>4 changed files:</h4>
<ul>
<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 class="file-stats">
<a href="#eba50f83701826b6bc6990a2ecb07d5959ac1f6d">
debian/patches/use_debian_packaged_redist.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/strelka/-/commit/db7dcedd9656926d870a2b46b8c597e49f1a9be7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">strelka (2.9.10+dfsg-1) UNRELEASED; 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"> * Initial release (Closes: #<bug>)</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> TODO: Prevent cmake from checking whether install can write to /usr</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 13 May 2020 16:55:22 +0200</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/strelka/-/commit/db7dcedd9656926d870a2b46b8c597e49f1a9be7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" 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="27" 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">@@ -27,7 +27,8 @@ Homepage: https://github.com/Illumina/strelka/</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Package: strelka</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> ${python3:Depends}</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Description: strelka2 germline and somatic small variant caller</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> Strelka2 is a fast and accurate small variant caller optimized for</span>
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<td class="diff-line-num new_line" data-linenumber="34" 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="LC34" class="line" lang="plaintext"> analysis of germline variation in small cohorts and somatic variation in</span>
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<li id="eba50f83701826b6bc6990a2ecb07d5959ac1f6d">
<a href="https://salsa.debian.org/med-team/strelka/-/commit/db7dcedd9656926d870a2b46b8c597e49f1a9be7#eba50f83701826b6bc6990a2ecb07d5959ac1f6d"><strong>debian/patches/use_debian_packaged_redist.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" 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="104" 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">@@ -104,3 +104,18 @@ Description: Use Debian packaged libs</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="diff"> message(STATUS "Detected workflow version: ${WORKFLOW_VERSION}")</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="diff"> file(WRITE ${CONFIG_FILE} "WORKFLOW_VERSION\t${WORKFLOW_VERSION}\n")</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="p">@@ -189,9 +189,9 @@</span> check_prefix()</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> # paths for binary components -- we don't currently change this from the non-binary components</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> set(THIS_EXEC_PREFIX "${CMAKE_INSTALL_PREFIX}")</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set(THIS_BINDIR "${THIS_EXEC_PREFIX}/bin")</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set(THIS_LIBDIR "${THIS_EXEC_PREFIX}/lib")</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set(THIS_LIBEXECDIR "${THIS_EXEC_PREFIX}/libexec")</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(THIS_BINDIR "${CMAKE_INSTALL_PREFIX}/bin")</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(THIS_LIBDIR "${CMAKE_INSTALL_PREFIX}/lib")</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(THIS_LIBEXECDIR "${CMAKE_INSTALL_PREFIX}/libexec")</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> # paths w/o architecture dependency</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> set(THIS_PYTHON_LIBDIR "${CMAKE_INSTALL_PREFIX}/lib/python")</span></pre>
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<a href="https://salsa.debian.org/med-team/strelka/-/commit/db7dcedd9656926d870a2b46b8c597e49f1a9be7#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">@@ -20,6 +20,8 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1 \</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> -DWORKFLOW_VERSION=$(DEB_VERSION_UPSTREAM)</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"># -DCMAKE_INSTALL_PREFIX=$(CURDIR)/debian/tmp</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> dh $@ --buildsystem=cmake</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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