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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/covpipe">Debian Med / covpipe</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/covpipe/-/commit/dd8b2601e94b4df4507986665a6b4d9361e44fb5">dd8b2601</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-03-25T21:41:39+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try hard do get at least a vague idea how a test could be run.
</pre>
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<h4>7 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#ddc317ba7cf8d9e99d9bf1627f5496463f4fc5aa">
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+
debian/patches/no_conda_for_tests.patch
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<li class="file-stats">
<a href="#e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
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+
debian/patches/python3.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#6bf1ea907d47c5d7ef0130ef1f1ff3f1ef267ac7">
debian/tests/control
→
debian/tests/control_deactivated
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/covpipe/-/commit/dd8b2601e94b4df4507986665a6b4d9361e44fb5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">covpipe (3.0.3-1) 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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<td class="new_line diff-line-num new" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> TODO: pangolin (https://salsa.debian.org/med-team/pangolin)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 25 Mar 2021 16:20:35 +0100</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/covpipe/-/commit/dd8b2601e94b4df4507986665a6b4d9361e44fb5#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,7 +6,10 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<td class="new_line diff-line-num" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> python3,</span>
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<td class="old_line diff-line-num old" data-linenumber="9" 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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<td class="new_line diff-line-num old" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> python3-setuptools</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3-biopython <!nocheck>,</span>
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<td class="new_line diff-line-num new" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> python3-pandas <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python3-yaml <!nocheck></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/covpipe</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/covpipe.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +19,10 @@ Rules-Requires-Root: no</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Package: covpipe</span>
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<td class="old_line diff-line-num" 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">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> ${misc:Depends},</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> snakemake,</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> python3-pysam,</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> python3-biopython</span>
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20
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Description: pipeline to generate consensus sequences from NGS reads</span>
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21
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> CovPipe is a pipeline to generate consensus sequences from NGS reads</span>
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22
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> based on a reference sequence. The pipeline is tailored to be used for</span>
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<li id="ddc317ba7cf8d9e99d9bf1627f5496463f4fc5aa">
<a href="https://salsa.debian.org/med-team/covpipe/-/commit/dd8b2601e94b4df4507986665a6b4d9361e44fb5#ddc317ba7cf8d9e99d9bf1627f5496463f4fc5aa"><strong>debian/patches/no_conda_for_tests.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Thu, 25 Mar 2021 16:20:35 +0100</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Try running without conda</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/tests/quicktest.sh</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/quicktest.sh</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span> eecho(){</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> echo $@ 1>&2</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if ! which activate > /dev/null ; then</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if ! which cat > /dev/null ; then</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> printf "%s\n"\</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> "Errro Encountered: You are currently in an active conda environment"\</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> " You need to either leave the environment and run this script again,"\</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -23,14 +23,14 @@</span> if ! type -a realpath > /dev/null; then</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> }</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> fi</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CONDA_ACTIVATE="$(which activate)"</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CONDA_ACTIVATE=""</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> CONDA_ACTIVE=0</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> activate_conda(){</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> echo $@</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> set +ue</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- source "$CONDA_ACTIVATE" --stack "$@"</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo source "$CONDA_ACTIVATE" --stack "$@"</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> set -ue</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> CONDA_ACTIVE=$((CONDA_ACTIVE+1))</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> echo CONDA ENVIRONMENTS "$CONDA_ACTIVE"</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">@@ -38,7 +38,7 @@</span> activate_conda(){</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> deactivate_conda(){</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> set +ue</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- conda deactivate</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo conda deactivate</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> set -ue</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> CONDA_ACTIVE=$((CONDA_ACTIVE-1))</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> echo ACTIVE CONDA ENVIRONMENTS $CONDA_ACTIVE</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="p">@@ -58,9 +58,6 @@</span> main(){</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> local PROXY=""</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> snake_args=( "" ) </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> local covpipe_package_exists=0</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if conda list | grep covpipe ; then</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- covpipe_package_exists=1</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fi </span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> local USE_MAMBA=0</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> if command -v mamba > /dev/null 2>&1; then</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ncov_minipipe.conda.setup/setup_env.sh</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ncov_minipipe.conda.setup/setup_env.sh</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="p">@@ -46,7 +46,7 @@</span> cp_if_file_exists(){</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> update_conda_or_install(){</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $CONDA_FRONTEND install \</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo $CONDA_FRONTEND install \</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> -c conda-forge -c bioconda -c defaults \</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> "python>=3.6.0" \</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> "snakemake>=5.26" \</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -66,12 +66,12 @@</span> cp "${ENV_SETUP}/d.env_vars.sh" "${DPATH</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> # Customization</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set +uEe</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-. activate "${ENVPATH}/"</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set -uEe</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python -m pip install "${DEV_MODE}" "${SNAKE_DIR}"</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set +uEe</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-conda deactivate</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set -uEe</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#set +uEe</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#. activate "${ENVPATH}/"</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#set -uEe</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#python -m pip install "${DEV_MODE}" "${SNAKE_DIR}"</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#set +uEe</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#conda deactivate</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#set -uEe</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> stop_setup</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> </span></pre>
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<li id="e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
<a href="https://salsa.debian.org/med-team/covpipe/-/commit/dd8b2601e94b4df4507986665a6b4d9361e44fb5#e246f69e945a7c2e9a8e25cfacfcac7714c92b69"><strong>debian/patches/python3.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/hash.py</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/hash.py</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> </span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> # hoelzerm@rki.de</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ncov_minipipe.conda.setup/env_setup/gb2fasta_gff.py</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ncov_minipipe.conda.setup/env_setup/gb2fasta_gff.py</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> # Copyright 2013-2014 Mitchell Stanton-Cook Licensed under the</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> # Educational Community License, Version 2.0 (the "License"); you may</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/covpipe/ncov_minipipe.py</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/covpipe/ncov_minipipe.py</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> from __future__ import print_function</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> from sys import version_info</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/covpipe_tools/update_pangolin.py</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/covpipe_tools/update_pangolin.py</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> import argparse</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> import re</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/TestData/References/search_ncbi_nuc.py</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/TestData/References/search_ncbi_nuc.py</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> from Bio import Entrez</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> import argparse</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/TestData/VCF_FILES/generate_vcf.py</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/TestData/VCF_FILES/generate_vcf.py</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/development_envs/setups/genbank2fasta.setup/env_setup/gb2fasta_gff.py</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/development_envs/setups/genbank2fasta.setup/env_setup/gb2fasta_gff.py</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> # Copyright 2013-2014 Mitchell Stanton-Cook Licensed under the</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> # Educational Community License, Version 2.0 (the "License"); you may</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/development_envs/setups/mummer.setup/env_setup/gb2fasta_gff.py</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/development_envs/setups/mummer.setup/env_setup/gb2fasta_gff.py</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> # Copyright 2013-2014 Mitchell Stanton-Cook Licensed under the</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> # Educational Community License, Version 2.0 (the "License"); you may</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/development_envs/setups/testDev.setup/env_setup/gb2fasta_gff.py</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/development_envs/setups/testDev.setup/env_setup/gb2fasta_gff.py</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> # Copyright 2013-2014 Mitchell Stanton-Cook Licensed under the</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> # Educational Community License, Version 2.0 (the "License"); you may</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/run_art.py</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/run_art.py</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> import os</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> import sys</span></pre>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/dd8b2601e94b4df4507986665a6b4d9361e44fb5#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">no_conda_for_tests.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">python3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/covpipe/-/commit/dd8b2601e94b4df4507986665a6b4d9361e44fb5#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">@@ -5,10 +5,9 @@</td>
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5
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5
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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">override_dh_fixperms:</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh_fixperms</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> find debian/*/usr/lib/python3/dist-packages -name "*.yaml" -exec chmod -x \{\} \;</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> find debian/*/usr/lib/python3/dist-packages <span class="idiff left">\( </span>-name "*.yaml" <span class="idiff right">-o -name "*.Rmd" -o -name "*.snake" -o -name "*.smk" \) </span>-exec chmod -x \{\} \;</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">#override_dh_auto_test:</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># do_stuff_for_testing</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">#endif</span></pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> tests/quicktest.sh -s</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">endif</span></pre>
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