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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/metabat">Debian Med / metabat</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabat/-/commit/4fe5dad1d46f3180a851aee6768321c200c2a1f8">4fe5dad1</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-28T20:28:04+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Attemot to tweak cmake
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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<a href="#ee54dc79014b3def963898e50c98877d46c6b27e">
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+
debian/patches/use_debian_packaged_libs.patch
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<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/metabat/-/commit/4fe5dad1d46f3180a851aee6768321c200c2a1f8#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" 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">@@ -8,10 +8,8 @@ endif()</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">message</span><span class="p">(</span><span class="s2" style="color: #d14;">"Installing </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_BUILD_TYPE</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> MetaBAT into </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_INSTALL_PREFIX</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_ROOT</span><span class="si" style="color: #d14;">}</span>/Modules/ExternalProject.cmake<span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>ZLIB REQUIRED<span class="p">)</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Find HTSlib. We find it with pkg-config, so it has static and dynamic libs by default.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="13" 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="LC13" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>PkgConfig REQUIRED<span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="14" 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="LC14" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">pkg_check_modules</span><span class="p">(</span>HTSlib REQUIRED htslib<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>cmake/zlib.cmake<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>cmake/htslib.cmake<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_STANDARD 11<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_STANDARD_REQUIRED ON<span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/metabat/-/commit/4fe5dad1d46f3180a851aee6768321c200c2a1f8#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">@@ -9,6 +9,8 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libboost-system-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libboost-filesystem-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libboost-serialization-dev,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> libboost-program-options-dev,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> libboost-iostreams-dev,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libhts-dev,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> pkg-config,</span>
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<a href="https://salsa.debian.org/med-team/metabat/-/commit/4fe5dad1d46f3180a851aee6768321c200c2a1f8#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">use_debian_packaged_libs.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/metabat/-/commit/4fe5dad1d46f3180a851aee6768321c200c2a1f8#ee54dc79014b3def963898e50c98877d46c6b27e"><strong>debian/patches/use_debian_packaged_libs.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Thu, 28 May 2020 17:21:42 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Use Debian packaged libraries</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/CMakeLists.txt</span>
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<pre style="margin: 0;">+<span id="LC6" 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="LC7" class="line" lang="diff"><span class="p">@@ -8,8 +8,10 @@</span> endif()</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> message("Installing ${CMAKE_BUILD_TYPE} MetaBAT into ${CMAKE_INSTALL_PREFIX}")</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> include(${CMAKE_ROOT}/Modules/ExternalProject.cmake)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-include(cmake/zlib.cmake)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-include(cmake/htslib.cmake)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+find_package(ZLIB REQUIRED)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Find HTSlib. We find it with pkg-config, so it has static and dynamic libs by default.</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+find_package(PkgConfig REQUIRED)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+pkg_check_modules(HTSlib REQUIRED htslib)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> set(CMAKE_CXX_STANDARD 11)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> set(CMAKE_CXX_STANDARD_REQUIRED ON)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">@@ -23,7 +25,7 @@</span> add_definitions(-D_XOPEN_SOURCE=700)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> set(PRE_CONFIGURE_FILE "metabat_version.h.in")</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> set(POST_CONFIGURE_FILE "metabat_version.h")</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-include(cmake/git-watcher.cmake)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# include(cmake/git-watcher.cmake)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> # using Clang</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;">--- a/src/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -36,7 +36,7 @@</span> set(targets metabat1 metabat2)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> foreach(target ${targets})</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> add_executable(${target} ${target}.cpp)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- add_dependencies(${target} htslib zlib check_git_repository)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ add_dependencies(${target} htslib zlib)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> target_link_libraries(${target} ${zlib_LIB} ${Boost_LIBRARIES} ${EXTRALIBS} ) </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> endforeach()</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -48,7 +48,7 @@</span> install(TARGETS ${targets}</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> set(targets jgi_summarize_bam_contig_depths contigOverlaps)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> foreach(target ${targets})</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> add_executable(${target} ${target}.cpp)</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- add_dependencies(${target} htslib zlib check_git_repository)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ add_dependencies(${target} htslib zlib)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> target_link_libraries(${target} ${htslib_LIB} ${zlib_LIB} ${Boost_LIBRARIES} ) </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> endforeach()</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span></pre>
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