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<h3>
Andreas Tille 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/b47226ad215b1d075b4f2f11f711fa6d02be2351">b47226ad</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-17T14:21:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix some installation issues
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/bbc12f16fa57fb43a8eb809517cfb36ba4e041b9">bbc12f16</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-17T14:22:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Allow pilon-non-free as alternative
</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/compare/0e522bb899e93d02ca18c753d5cdfcd0134a00f3...bbc12f16fa57fb43a8eb809517cfb36ba4e041b9#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +11,7 @@ Build-Depends: debhelper (>= 11~),</td>
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11
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<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">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> ncbi-blast+,</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> pilon,</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> pilon<span class="idiff left right"> | pilon-non-free</span>,</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> racon,</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> samtools,</span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> spades,</span>
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<br>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/unicycler/compare/0e522bb899e93d02ca18c753d5cdfcd0134a00f3...bbc12f16fa57fb43a8eb809517cfb36ba4e041b9#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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="17" 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">@@ -17,11 +17,14 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> find . -name "*.o" -delete</span>
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<td class="diff-line-num old_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext"> find . -name "*.so" -delete</span>
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<td class="diff-line-num old_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext"> find . -name __pycache__ -type d | xargs rm -rf</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> rm -rf .pybuild unicycler.egg-info</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> # building the dynamic library requires extra make call</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> make</span>
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<pre style="margin: 0;">+<span id="LC26" 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="LC27" class="line" lang="plaintext"> cp -a unicycler/cpp_functions.so `dirname $$(find .pybuild -name cpp_wrappers.py)`</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> BUILDPATH=$(shell pybuild --print build_dir --interpreter python3) ; \</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,3 +32,8 @@ override_dh_auto_test:</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> ln -s $(CURDIR)/unicycler-runner.py $${BUILDPATH} ; \</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> cp -a unicycler/*.so $${BUILDPATH}/$(PYBUILD_NAME) ; \</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> PYTHONPATH=$${BUILDPATH}/$(PYBUILD_NAME) dh_auto_test || true</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">override_dh_link:</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> dh_link</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> # symlink versioned shared lib to make it found</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> ln -s `basename $$(find debian -name "cpp_functions*.so")` `dirname $$(find debian -name "cpp_functions*.so")`/cpp_functions.so</span></pre>
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