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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/quast">Debian Med / quast</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/quast/-/commit/4ad40d3fbf2fe943311d95ebb2b6c8c098763215">4ad40d3f</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2021-08-25T01:16:16+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working on lintian erros - tests seem fine
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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+
debian/quast.links
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/quast/-/commit/4ad40d3fbf2fe943311d95ebb2b6c8c098763215#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">quast (5.0.2+dfsg-1) UNRELEASED; urgency=medium</span>
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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"> * Initial release (Closes: #963618)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * Builds, but tests fail - see d/TODO</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Seems fine, only some Lintian errors for embedded JavaScript need to be</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> addressed:</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">E: quast source: source-is-missing quast_libs/html_saver/static/bootstrap/bootstrap-tooltip-5px-lower.min.js</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">E: quast source: source-is-missing quast_libs/html_saver/static/bootstrap/bootstrap.min.js</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">E: quast source: source-is-missing quast_libs/html_saver/static/flot/jquery.flot.js line length is 2964 characters (>512)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">E: quast source: source-is-missing quast_libs/html_saver/static/flot/jquery.flot.navigate.js line length is 1984 characters (>512)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">E: quast source: source-is-missing quast_libs/html_saver/static/flot/jquery.flot.pie.js line length is 259 characters (>256)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">E: quast source: source-is-missing quast_libs/html_saver/static/flot/jquery.flot.resize.js line length is 863 characters (>512)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">E: quast source: source-is-missing quast_libs/html_saver/static/ie_html5.js line length is 2252 characters (>512)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">E: quast source: source-is-missing quast_libs/html_saver/static/jquery-1.7.2.min.js</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">W: quast: embedded-javascript-library usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery.css please use libjs-jquery</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">W: quast: no-manual-page usr/bin/icarus.py</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">W: quast: no-manual-page usr/bin/metaquast.py</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">W: quast: no-manual-page usr/bin/quast-lg.py</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">W: quast: no-manual-page usr/bin/quast.py</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"> -- Andreas Tille <tille@debian.org> Wed, 22 Apr 2020 15:30:18 +0200</span></pre>
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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">@@ -17,7 +17,6 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"># hmmer,</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"># bwa,</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"># bedtools,</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"># busco,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># ncbi-blast+,</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"># sambamba</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Standards-Version: 4.5.0</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">@@ -45,7 +44,10 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> busco,</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> tigr-glimmer,</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> python-matplotlib,</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> python3-joblib</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> python3-joblib,</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> libjs-excanvas,</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> libjs-jquery,</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> libjs-jquery-ui</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">Description: Quality Assessment Tool for Genome Assemblies</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> project. It works both with and without a given reference genome.</span>
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<a href="https://salsa.debian.org/med-team/quast/-/commit/4ad40d3fbf2fe943311d95ebb2b6c8c098763215#f11dce8437239d9adad6cc6da706e11b9e06314b"><strong>debian/quast.links</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/javascript/excanvas/excanvas.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/flot/excanvas.js</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">usr/share/javascript/excanvas/excanvas.min.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/flot/excanvas.min.js</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">usr/share/javascript/jquery/jquery.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/flot/jquery.js</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">usr/share/javascript/jquery/jquery.min.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/flot/jquery.min.js</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">usr/share/javascript/jquery-ui/ui/jquery-1-7.min.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery-1.7.2.min.js</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">usr/share/javascript/jquery/jquery.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery-1.8.2.js</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">usr/share/javascript/jquery/jquery.min.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery-1.8.2.min.js</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">usr/share/javascript/jquery-ui/jquery-ui.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery-ui.js</span></pre>
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<a href="https://salsa.debian.org/med-team/quast/-/commit/4ad40d3fbf2fe943311d95ebb2b6c8c098763215#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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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"><span class="idiff left right"># </span>DH_VERBOSE := 1</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"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> rm -f quast_libs/busco/hmmsearch</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> find quast_libs -name "*.o" -delete</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> rm -f quast_libs/glimmer/glimmerhmm quast_libs/glimmer/src/make.err quast_libs/glimmer/src/make.log</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> rm -f quast_libs/version.py</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> # files generated while testing</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> rm -f quast_test_output/quast.log quast_test_output/quast_corrected_input/contigs_1.fasta quast_test_output/quast_corrected_input/contigs_2.fasta quast_test_output/quast_corrected_input/reference.fasta</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> find debian -name LICENSE.txt -delete</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">@@ -22,3 +13,22 @@ override_dh_auto_test:</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> PATH=$PATH:. ./setup.py test</span>
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24
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<td class="new_line diff-line-num" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">endif</span>
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<td class="new_line diff-line-num new" data-linenumber="16" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" 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"> dh_auto_clean</span>
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<td class="new_line diff-line-num new" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> rm -rf quast_test_output</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> rm -f quast_libs/busco/hmmsearch</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> find quast_libs -name "*.o" -delete</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> rm -f quast_libs/glimmer/glimmerhmm quast_libs/glimmer/src/make.err quast_libs/glimmer/src/make.log</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> rm -f quast_libs/version.py</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> #$(MAKE) -C quast_libs/MUMmer/ clean >/dev/null 2>/dev/null</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> rm -f quast_libs/MUMmer/make.*</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> #$(MAKE) -C quast_libs/glimmer/src/ clean >/dev/null 2>/dev/null</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> rm -f quast_libs/glimmer/src/make.*</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> rm -f *.pyc</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> rm -f quast_libs/*.pyc</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> rm -f quast_libs/html_saver/*.pyc</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> rm -f quast_libs/site_packages/*/*.pyc</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> #$(MAKE) -C quast_libs/bwa clean >/dev/null 2>/dev/null</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> rm -rf quast_libs/gridss*</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> rm -rf quast_libs/blast</span></pre>
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