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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/a3b90a3a5c00e9b83a48c7746b4aa598202c8642">a3b90a3a</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2018-09-27T10:51:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Provide upstream sample_data in a separate package
</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
<li class="file-stats">
<a href="#439647366ba405215fe949c8f5a89c1ac2cc762a">
<span class="new-file">
+
debian/unicycler-data.install
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</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/unicycler/commit/a3b90a3a5c00e9b83a48c7746b4aa598202c8642#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<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">@@ -27,17 +27,30 @@ Architecture: any</td>
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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="LC27" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="28" 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="LC28" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="29" 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="LC29" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> default-jre,</span>
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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">
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> bowtie2,</span>
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<td class="diff-line-num old old_line" data-linenumber="32" 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="LC32" class="line" lang="plaintext"> freebayes,</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="LC33" class="line" lang="plaintext"> ncbi-blast+,</span>
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<td class="diff-line-num old_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"> pilon,</span>
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<td class="diff-line-num old_line" data-linenumber="35" 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="LC35" class="line" lang="plaintext"> racon,</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> samtools,</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="LC37" class="line" lang="plaintext"> spades</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Recommends: unicycler-data</span>
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<td class="diff-line-num old_line" data-linenumber="38" 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="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">
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Description: hybrid assembly pipeline for bacterial genomes</span>
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> Unicycler is an assembly pipeline for bacterial genomes. It can assemble</span>
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> Illumina-only read sets where it functions as a SPAdes-optimiser. It can</span>
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<td class="diff-line-num new_line" data-linenumber="42" 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="LC42" class="line" lang="plaintext"> also assembly long-read-only sets (PacBio or Nanopore) where it runs a</span>
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<td class="diff-line-num old_line" data-linenumber="42" 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="43" 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="LC43" class="line" lang="plaintext"> miniasm+Racon pipeline. For the best possible assemblies, give it both</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> Illumina reads and long reads, and it will conduct a hybrid assembly.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="46" 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="LC46" class="line" lang="plaintext">Package: unicycler-data</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">Description: hybrid assembly pipeline for bacterial genomes (data package)</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> Unicycler is an assembly pipeline for bacterial genomes. It can assemble</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> Illumina-only read sets where it functions as a SPAdes-optimiser. It can</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> also assembly long-read-only sets (PacBio or Nanopore) where it runs a</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> miniasm+Racon pipeline. For the best possible assemblies, give it both</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> Illumina reads and long reads, and it will conduct a hybrid assembly.</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> This package contains architecture independent data for unicycler.</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/unicycler/commit/a3b90a3a5c00e9b83a48c7746b4aa598202c8642#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">@@ -2,20 +2,16 @@</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"># 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"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"># Build time tests are flaky</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># export DH_BUILD_MAINT_OPTIONS=nocheck</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># But rather run the tests and ignore errors than no tests at all.</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># Thus we might have a look into build-logs to see what is failing</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</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">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">export PYBUILD_NAME=unicycler</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" 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="LC12" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST=cp -a unicycler-runner.py {build_dir}; \</span>
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17
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> cp -a unicycler/cpp_functions.so {build_dir}/unicycler; \</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> cp -<span class="idiff left right">r</span> sample_data {build_dir}</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> cp -<span class="idiff left right">a</span> sample_data {build_dir}</span>
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19
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">export PYBUILD_AFTER_TEST=rm {build_dir}/unicycler-runner.py; \</span>
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20
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> rm -r {build_dir}/sample_data; \</span>
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21
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> rm -r {build_dir}/unicycler/__pycache__</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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>
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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">@@ -33,3 +29,9 @@ override_dh_auto_clean:</td>
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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="LC30" class="line" lang="plaintext"> make</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> dh_auto_install --destdir=debian/$(PYBUILD_NAME)</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_python3:</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> dh_python3 --no-ext-rename</span></pre>
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<a href="https://salsa.debian.org/med-team/unicycler/commit/a3b90a3a5c00e9b83a48c7746b4aa598202c8642#439647366ba405215fe949c8f5a89c1ac2cc762a"><strong>debian/unicycler-data.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">sample_data</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">unicycler</span><span class="o" style="font-weight: 600;">-</span><span class="nx">data</span></span></pre>
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