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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/bowtie2">Debian Med / bowtie2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/7bfaa165994c4309babde7db98c033a355393fdf">7bfaa165</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-15T09:18:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set M64_FLAG and POPCNT_CAPABILITY; 64bit archs only
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/42ade843e40b9e0b7639b147cef2beb00d72b19b">42ade843</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-15T15:16:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix building in with cowdancer or eatmydata
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/2b056b8c4e3314ea40cdce60ab774da678a5de50">2b056b8c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-15T15:16:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add missing ${perl:Depends}
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/1cb4b2ab49f3a058f0de9240f448fa42fb33c72e">1cb4b2ab</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-15T15:16:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">build everywhere again
</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/d06dfdbed5448bd1387ca58dafdd88c50cd1431a...1cb4b2ab49f3a058f0de9240f448fa42fb33c72e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -2,6 +2,10 @@ bowtie2 (2.3.5.1-3) unstable; urgency=medium</td>
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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"> * Team upload.</span>
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<td class="diff-line-num new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> * Enable all architectures via simde.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Unset M64_FLAG and POPCNT_CAPABILITY on non AMD64 archs.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * debian/rules: Fix testing in with cowdancer or eatmydata by unsetting</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> LD_PRELOAD (the address sanitizer must be first in the library list)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Added missing ${perl:Depends} for the bowtie2 binary package</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Sat, 14 Dec 2019 13:42:14 +0100</span>
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<td class="diff-line-num new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/d06dfdbed5448bd1387ca58dafdd88c50cd1431a...1cb4b2ab49f3a058f0de9240f448fa42fb33c72e#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" 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="23" 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">@@ -23,7 +23,8 @@ Package: bowtie2</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Depends: python3,</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> ${shlibs:Depends}</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> ${perl:Depends}</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Suggests: bowtie2-examples</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Description: ultrafast memory-efficient short read aligner</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> is an ultrafast and memory-efficient tool for aligning sequencing reads</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/d06dfdbed5448bd1387ca58dafdd88c50cd1431a...1cb4b2ab49f3a058f0de9240f448fa42fb33c72e#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,8 +13,11 @@ export DEB_CXXFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">EXTRA_OPTIONS =</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">ifneq ($(DEB_HOST_ARCH),amd64)</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> EXTRA_OPTIONS = NO_TBB=1</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> EXTRA_OPTIONS += NO_TBB=1 POPCNT_CAPABILITY= M64_FLAG=</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> EXTRA_OPTIONS += POPCNT_CAPABILITY=1 M64_FLAG=-m64</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">export EXTRA_OPTIONS</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">%:</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">@@ -36,7 +39,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> bowtie2-align-l-sanitized \</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> bowtie2-build-s-sanitized \</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> bowtie2-build-l-sanitized</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> make -j1 test</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>make -j1 test</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">override_dh_auto_install:</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">@@ -47,15 +50,15 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align-*"</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-build "wrapper for $(pkg)-build-*"</span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-build-l "building a colorspace index for $(pkg)"</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-build-s "building a colorspace index for $(pkg)"</span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-inspect "wrapper for $(pkg)-inspect-* index"</span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-inspect-l "extracts information from a $(pkg) index"</span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-inspect-s "extracts information from a $(pkg) index"</span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-align-l "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"</span>
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<td class="diff-line-num old old_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> debian/help2man-wrapper $(pkg)-align-s "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align-*"</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-build "wrapper for $(pkg)-build-*"</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-build-l "building a colorspace index for $(pkg)"</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-build-s "building a colorspace index for $(pkg)"</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-inspect "wrapper for $(pkg)-inspect-* index"</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-inspect-l "extracts information from a $(pkg) index"</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-inspect-s "extracts information from a $(pkg) index"</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-align-l "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> <span class="idiff left right">env --unset=LD_PRELOAD </span>debian/help2man-wrapper $(pkg)-align-s "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"</span>
</pre>
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59
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> rm -f $(CURDIR)/debian/$(pkg)/usr/bin/bowtie2-buildc</span>
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60
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"></span>
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61
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">override_dh_installchangelogs:</span>
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