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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/resfinder">Debian Med / resfinder</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/resfinder/commit/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6">5982f45b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-11-15T09:17:47Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Package only Python version, provide example data in examples package
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
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debian/README.Debian
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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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<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
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−
debian/install
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<li class="file-stats">
<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
debian/lintian-overrides
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<li class="file-stats">
<a href="#cf69f07e6f91dc2cba44196ddad9453598193a0c">
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+
debian/resfinder-example.install
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<li class="file-stats">
<a href="#e63263210b9156ba404e775f941345f7b4dc919c">
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debian/resfinder.install
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<li class="file-stats">
<a href="#d96662f897509f5b5aebd957a04c5432599b03b2">
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debian/resfinder.links
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<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/resfinder/commit/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">resfinder for Debian</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>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Quoting the resfinder doc:</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"> The ResFinder service contains one perl script *resfinder.pl* which is the</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> script of the latest version of the ResFinder service. ResFinder identifies</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> acquired antimicrobial resistance genes in total or partial sequenced isolates</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> of bacteria.</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"> This repository also contains a python script *resfinder.py* which is a new version</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> of ResFinder, but not yet running on the CGE server. This program was added because</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> it uses a newer version of blastn, which, in contrary from the blastall version</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> that the perl script uses, is avail to download.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">The user who requested this package is just interested in the Python version of</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">redfinder thus only this script is packaged.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 07 Nov 2019 12:41:11 +0100</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/resfinder/commit/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">resfinder (3.2-1) 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: #<bug>)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> TODO: Clarify relation between *.pl and *.py</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"> -- Andreas Tille <tille@debian.org> Thu, 07 Nov 2019 12:41:11 +0100</span></pre>
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<a href="https://salsa.debian.org/med-team/resfinder/commit/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -4,16 +4,16 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> dh-python</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python3</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Standards-Version: 4.4.1</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/resfinder</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/resfinder.git</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: https://bitbucket.org/genomicepidemiology/resfinder</span>
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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">Package: resfinder</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Depends: ${perl:Depends},</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> bioperl,</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> ncbi-blast+-legacy</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">@@ -27,3 +27,20 @@ Description: identifies acquired antimicrobial resistance genes</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> from four different sequencing platforms. The method was evaluated on</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> 1862 GenBank files containing 1411 different resistance genes, as well</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> as on 23 de-novo-sequenced isolates.</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">Package: resfinder-example</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Recommends: resfinder</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Description: identifies acquired antimicrobial resistance genes (example data)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> ResFinder identifies acquired antimicrobial resistance genes in total or</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> partial sequenced isolates of bacteria.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> ResFinder that uses BLAST for identification of acquired antimicrobial</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> resistance genes in whole-genome data. As input, the method can use both</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> pre-assembled, complete or partial genomes, and short sequence reads</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> from four different sequencing platforms. The method was evaluated on</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> 1862 GenBank files containing 1411 different resistance genes, as well</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> as on 23 de-novo-sequenced isolates.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> This package contains example data to test resfinder.</span></pre>
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<a href="https://salsa.debian.org/med-team/resfinder/commit/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">*.py /usr/bin</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">*.pl /usr/bin</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># see discussion on Debian Med mailing list</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"># https://lists.debian.org/debian-med/2018/06/msg00042.html</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># and following mails in thread</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">resfinder: script-with-language-extension usr/bin/resfinder.p<span class="idiff left right">l</span></span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">resfinder: script-with-language-extension usr/bin/resfinder.p<span class="idiff left right">y</span></span></pre>
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<li id="cf69f07e6f91dc2cba44196ddad9453598193a0c">
<a href="https://salsa.debian.org/med-team/resfinder/commit/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6#cf69f07e6f91dc2cba44196ddad9453598193a0c"><strong>debian/resfinder-example.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">.</span><span class="nx">fsa</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">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">resfinder</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span></pre>
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<li id="e63263210b9156ba404e775f941345f7b4dc919c">
<a href="https://salsa.debian.org/med-team/resfinder/commit/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6#e63263210b9156ba404e775f941345f7b4dc919c"><strong>debian/resfinder.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="o" style="font-weight: 600;">*.</span><span class="nx">py</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">resfinder</span></span></pre>
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<li id="d96662f897509f5b5aebd957a04c5432599b03b2">
<a href="https://salsa.debian.org/med-team/resfinder/commit/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6#d96662f897509f5b5aebd957a04c5432599b03b2"><strong>debian/resfinder.links</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/resfinder/resfinder.py usr/bin/resfinder.py</span></pre>
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