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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/unicycler">Debian Med / unicycler</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/01c6541c861301a856a6e35db2e08d34411ae68b">01c6541c</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2018-09-07T17:01:06Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Modify debian/rules
</pre>
</li>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/unicycler/commit/01c6541c861301a856a6e35db2e08d34411ae68b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" 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="9" 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">@@ -9,7 +9,6 @@ Build-Depends: debhelper (>= 11~),</td>
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<td class="diff-line-num new_line" data-linenumber="9" 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">
9
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<td class="diff-line-num old_line" data-linenumber="10" 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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<td class="diff-line-num new_line" data-linenumber="10" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> default-jdk,</span>
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<td class="diff-line-num old_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">
11
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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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> bowtie2,</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> freebayes,</span>
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<td class="diff-line-num old_line" data-linenumber="13" 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">
13
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> ncbi-blast+,</span>
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<td class="diff-line-num old_line" data-linenumber="14" 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">
14
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> pilon,</span>
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<td class="diff-line-num old_line" data-linenumber="15" 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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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> racon,</span>
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<br>
</li>
<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/unicycler/commit/01c6541c861301a856a6e35db2e08d34411ae68b#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">@@ -2,7 +2,16 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">export PYBUILD_NAME=unicycler</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"># NOTE: All build steps are described in setup.py:UnicyclerInstall</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># copy all nacessary data before testing and make clean after the testing</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST=cp -a unicycler-runner.py {build_dir}; \</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> cp -a unicycler/cpp_functions.so {build_dir}/unicycler; \</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> cp -r sample_data {build_dir}</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">export PYBUILD_AFTER_TEST=rm {build_dir}/unicycler-runner.py; \</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> rm -r {build_dir}/sample_data; \</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> rm -r {build_dir}/unicycler/__pycache__</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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7
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"># Build time tests are flaky</span>
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8
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">export DH_BUILD_MAINT_OPTIONS=nocheck</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">@@ -15,27 +24,11 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">override_dh_auto_clean:</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> echo "Avoid: command 'UnicyclerClean' has no such option 'all'"</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> find . -name "*.o" -delete</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> find . -name "*.so" -delete</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> find . -name __pycache__ -type d | xargs rm -rf</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> rm -rf .pybuild unicycler.egg-info</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> make distclean</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> # building the dynamic library requires extra make call</span>
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27
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> make</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> # for some reason it also needs to be manually moved</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> cp -a unicycler/cpp_functions.so `dirname $$(find .pybuild -name cpp_wrappers.py)`</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> BUILDPATH=$(shell pybuild --print build_dir --interpreter python3) ; \</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> for bp in .pybuild/cpython*$(DEB_SOURCE)/build ; do \</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> ln -s $(CURDIR)/sample_data $${bp} ; \</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> ln -s $(CURDIR)/unicycler-runner.py $${bp} ; \</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> cp -a unicycler/*.so $${bp}/$(PYBUILD_NAME) ; \</span>
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<td class="diff-line-num old old_line" data-linenumber="37" 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">
37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> done ; \</span>
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<td class="diff-line-num old old_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> PYTHONPATH=$${BUILDPATH}/$(PYBUILD_NAME) dh_auto_test # || true</span>
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<td class="diff-line-num new old_line" data-linenumber="39" 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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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> dh_auto_build</span>
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<td class="diff-line-num old_line" data-linenumber="39" 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">
39
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<td class="diff-line-num new_line" data-linenumber="32" 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">
32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="40" 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">
40
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">override_dh_link:</span>
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<td class="diff-line-num old_line" data-linenumber="41" 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">
41
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> dh_link</span>
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