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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/idseq-dag">Debian Med / idseq-dag</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/idseq-dag/-/commit/aae9c062354c8644ea70e4c7bb524c835dfb6c7e">aae9c062</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-15T13:15:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make examples available for test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/idseq-dag/-/commit/b81ec7be5d860b19113fd10c8f88dbf2aa94a6ef">b81ec7be</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-15T13:22:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Users do not have permissions to write to /mnt by default so change the default output dir to /var/tmp/idseq
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/idseq-dag/-/commit/8f481dbe23e1809346aaa5c8f9d00ca2a91755e6">8f481dbe</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-15T17:02:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Seems bowtie2 is definitely needed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/idseq-dag/-/commit/4507a00935ca0916d011c421c78433883db16420">4507a009</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-15T17:02:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try making tests with changed default_dir succeed but failed.
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
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<li class="file-stats">
<a href="#3d0f32a641768cab78168d91ef1600e20c22979a">
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+
debian/patches/set_default_output_dir_var_tmp.patch
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</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/idseq-dag/-/compare/fe29b3b2adeaefe137e4887e251f12880d7cc8a1...4507a00935ca0916d011c421c78433883db16420#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -19,7 +19,8 @@ Package: python3-idseq-dag</td>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Architecture: all</span>
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<td class="diff-line-num new_line" data-linenumber="20" 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">Depends: ${python3:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="21" 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="21" 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="LC21" class="line" lang="plaintext"> ${misc:Depends},</span>
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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC22" class="line" lang="plaintext"> python3-boto3</span>
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<td class="diff-line-num new old_line" data-linenumber="23" 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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<td class="diff-line-num new new_line" data-linenumber="22" 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="LC22" class="line" lang="plaintext"> python3-boto3,</span>
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<td class="diff-line-num new old_line" data-linenumber="23" 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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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="plaintext"> bowtie2</span>
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<td class="diff-line-num new_line" data-linenumber="24" 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="LC24" class="line" lang="plaintext">Description: Pipeline engine for IDseq (Python 3)</span>
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<td class="diff-line-num old_line" data-linenumber="24" 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="25" 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="LC25" class="line" lang="plaintext"> Idseq_dag is the pipeline execution engine for idseq</span>
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<td class="diff-line-num old_line" data-linenumber="25" 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="26" 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="LC26" class="line" lang="plaintext"> (see idseq.net). It is a pipelining system that implements</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/idseq-dag/-/compare/fe29b3b2adeaefe137e4887e251f12880d7cc8a1...4507a00935ca0916d011c421c78433883db16420#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">set_default_output_dir_var_tmp.patch</span></pre>
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<li id="3d0f32a641768cab78168d91ef1600e20c22979a">
<a href="https://salsa.debian.org/med-team/idseq-dag/-/compare/fe29b3b2adeaefe137e4887e251f12880d7cc8a1...4507a00935ca0916d011c421c78433883db16420#3d0f32a641768cab78168d91ef1600e20c22979a"><strong>debian/patches/set_default_output_dir_var_tmp.patch</strong></a>
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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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Wed, 15 Apr 2020 13:21:24 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Users do not have permissions to write to /mnt by default so change the</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> default output dir to /var/tmp/idseq</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/idseq_dag/engine/pipeline_flow.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/idseq_dag/engine/pipeline_flow.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -15,8 +15,8 @@</span> import idseq_dag.util.count as count</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> from idseq_dag.util.trace_lock import TraceLock</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> from idseq_dag.engine.pipeline_step import PipelineStep, InvalidInputFileError</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </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;">-DEFAULT_OUTPUT_DIR_LOCAL = '/mnt/idseq/results/%d' % os.getpid()</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-DEFAULT_REF_DIR_LOCAL = '/mnt/idseq/ref'</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+DEFAULT_OUTPUT_DIR_LOCAL = '/var/tmp/idseq/results/%d' % os.getpid()</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+DEFAULT_REF_DIR_LOCAL = '/var/tmp/idseq/ref'</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> PURGE_SENTINEL_DIR = DEFAULT_REF_DIR_LOCAL + "/purge_sentinel"</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> PURGE_SENTINEL = PURGE_SENTINEL_DIR + "/purge_nothing_newer_than_me"</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -266,7 +266,7 @@</span> class PipelineFlow(object):</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> log.log_event("Reference downloads cache efficiency report", values=structured_report)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> idseq_dag.util.s3.make_space() # make sure to touch this stage's files before deleting LRU ones</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # N.B. the default results folder /mnt/idseq/results is removed by the aegea</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # N.B. the default results folder /var/tmp/idseq/results is removed by the aegea</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> # command script driven through idseq-web --- so we don't have to worry about</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> # clearing that space here</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </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;">--- a/idseq_dag/steps/fetch_tax_info.py</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;">+++ b/idseq_dag/steps/fetch_tax_info.py</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -32,7 +32,7 @@</span> class PipelineStepFetchTaxInfo(PipelineS</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> id2namedict = {}</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> if namecsv:</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> # This is fetching a reference without fetch_reference; but ok because does not run from the actual pipeline</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- namecsvf = s3.fetch_from_s3(namecsv, "/mnt/idseq/ref")</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ namecsvf = s3.fetch_from_s3(namecsv, "/var/tmp/idseq/ref")</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> with open(namecsvf, 'r') as namef:</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> for line in namef:</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> fields = line.rstrip().split(",")</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/idseq_dag/steps/run_bowtie2.py</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/idseq_dag/steps/run_bowtie2.py</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="p">@@ -77,10 +77,10 @@</span> class PipelineStepRunBowtie2(PipelineCou</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> bowtie2_params.extend(['-U', input_fas[0]])</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> # Example:</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # bowtie2 -q -x /mnt/idseq/ref/bowtie2_genome/hg38_phiX_rRNA_mito_ERCC -f \</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # --very-sensitive-local -S /mnt/idseq/results/589/bowtie2_human.sam \</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # bowtie2 -q -x /var/tmp/idseq/ref/bowtie2_genome/hg38_phiX_rRNA_mito_ERCC -f \</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # --very-sensitive-local -S /var/tmp/idseq/results/589/bowtie2_human.sam \</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> # -p 32 \</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # -1 /mnt/idseq/results/589/unmapped_human_1.fa -2 /mnt/idseq/results/589/unmapped_human_2.fa</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # -1 /var/tmp/idseq/results/589/unmapped_human_1.fa -2 /var/tmp/idseq/results/589/unmapped_human_2.fa</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> command.execute(</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> command_patterns.SingleCommand(</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> cmd='bowtie2',</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unit/steps/test_download_accessions.py</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/unit/steps/test_download_accessions.py</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="p">@@ -24,9 +24,9 @@</span> class TestDownloadAccessions(unittest.Te</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> ]</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> ],</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> output_files=["assembly/nr.refseq.fasta"],</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- output_dir_local="/mnt/idseq/results",</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ output_dir_local="/var/tmp/idseq/results",</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> output_dir_s3="s3://dummy_bucket",</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ref_dir_local="/mnt/idseq/ref/",</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ref_dir_local="/var/tmp/idseq/ref/",</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> additional_files={</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> "lineage_db": "s3://idseq-database/taxonomy/2018-12-01/taxid-lineages.sqlite3",</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> "loc_db": "s3://idseq-database/alignment_data/2018-12-01/nr_loc.sqlite3"</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="p">@@ -75,4 +75,4 @@</span> class TestDownloadAccessions(unittest.Te</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> result = self.step._fix_ncbi_record(accession_data)</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> self.assertEqual(result, expected_result)</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;">- </span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</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;">+ </span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/idseq_step_setup.py</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;">+++ b/tests/idseq_step_setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="p">@@ -30,10 +30,10 @@</span> class IdseqStepSetup(object):</span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> "testrun_%s_%d_%d" % (step_name,</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> int(paired),</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> int(time.time())))</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- result_dir_local = "/mnt/idseq/results/%s_%d/%d" % (step_name,</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ result_dir_local = "/var/tmp/idseq/results/%s_%d/%d" % (step_name,</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> int(paired),</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> os.getpid())</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ref_dir_local = '/mnt/idseq/ref'</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ref_dir_local = '/var/tmp/idseq/ref'</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> command.make_dirs(result_dir_local)</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> command.make_dirs(ref_dir_local)</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="p">@@ -77,8 +77,8 @@</span> class IdseqStepSetup(object):</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> od = output_dir_s3 or dag["output_dir_s3"]</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> output_dir_s3 = os.path.join(od,</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> f"testrun_{step_name}_{int(time.time())}")</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- result_dir_local = f"/mnt/idseq/results/{step_name}/{os.getpid()}"</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ref_dir_local = '/mnt/idseq/ref'</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ result_dir_local = f"/var/tmp/idseq/results/{step_name}/{os.getpid()}"</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ref_dir_local = '/var/tmp/idseq/ref'</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> command.make_dirs(result_dir_local)</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> command.make_dirs(ref_dir_local)</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/idseq-dag/-/compare/fe29b3b2adeaefe137e4887e251f12880d7cc8a1...4507a00935ca0916d011c421c78433883db16420#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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1
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export PYBUILD_NAME=idseq-dag</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST=cp -r {dir}/examples {build_dir}</span>
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2
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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3
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<td class="diff-line-num new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">%:</span>
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<td class="diff-line-num old_line" data-linenumber="4" 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">
4
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<td class="diff-line-num new_line" 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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<td class="diff-line-num old_line" data-linenumber="5" 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">
5
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<td class="diff-line-num new_line" data-linenumber="9" 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">
9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<td class="diff-line-num new old_line" data-linenumber="6" 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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<td class="diff-line-num new new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">override_dh_auto_test:</span>
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<td class="diff-line-num new old_line" data-linenumber="6" 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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<td class="diff-line-num new new_line" 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">
11
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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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<td class="diff-line-num new old_line" data-linenumber="6" 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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<td class="diff-line-num new new_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> mkdir -p /var/tmp/idseq</span>
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<td class="diff-line-num new old_line" data-linenumber="6" 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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<td class="diff-line-num new new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> dh_auto_test</span>
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<td class="diff-line-num new old_line" data-linenumber="6" 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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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">endif</span></pre>
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