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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/mapping-pipeline">Debian Med / mapping-pipeline</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapping-pipeline/commit/19181f419058eaa2acf12f04fbefe68bfd09cd6a">19181f41</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2017-02-23T14:23:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix permissions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapping-pipeline/commit/16509067b43f7871e34b9ed206a4147a20ea2697">16509067</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2017-02-24T08:50:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some fixes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapping-pipeline/commit/362142266a0d580638bfbefa7c9652cf05760cf2">36214226</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2017-02-24T08:51:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CWL-runner
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#c748dc6dee691a1bf4f47c8ae0a71d23e8a40805">
<span class="new-file">
+
debian/cwl-runner/cwl-runner
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</li>
<li class="file-stats">
<a href="#bdab0d370fd575df6b6829cfaa33bdff4ad1b0ba">
<span class="new-file">
+
debian/patches/path_to_report.tex.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#dab3de00a53f9de2b5f006a799a73a524a2a7cee">
<span class="new-file">
+
debian/patches/picard.patch
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</li>
<li class="file-stats">
<a href="#e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
debian/patches/python3.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</ul>
<h4>Changes:</h4>
<li id="c748dc6dee691a1bf4f47c8ae0a71d23e8a40805">
<a href="https://salsa.debian.org/med-team/mapping-pipeline/compare/124837ebe731976a79e8a88e36a721dc4bd12894...362142266a0d580638bfbefa7c9652cf05760cf2#c748dc6dee691a1bf4f47c8ae0a71d23e8a40805"><strong>debian/cwl-runner/cwl-runner</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#!/home/dabrowskiw/cwl/cwl_vw/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cwltool.main</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">main</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="s" style="color: #d14;">r'(-script\.pyw|\.exe)?$'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">main</span><span class="p">())</span></span></pre>
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</li>
<li id="bdab0d370fd575df6b6829cfaa33bdff4ad1b0ba">
<a href="https://salsa.debian.org/med-team/mapping-pipeline/compare/124837ebe731976a79e8a88e36a721dc4bd12894...362142266a0d580638bfbefa7c9652cf05760cf2#bdab0d370fd575df6b6829cfaa33bdff4ad1b0ba"><strong>debian/patches/path_to_report.tex.patch</strong></a>
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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/mapping.py</span></span>
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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/mapping.py</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -134,10 +134,10 @@ class MAPPING:</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> # self.env = jinja2.Environment()</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> # self.env.loader = jinja2.FileSystemLoader('.')</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # self.template = self.env.get_template(os.path.join(os.path.dirname(__file__), 'report.tex'))</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # self.template = self.env.get_template(os.path.join('/usr/share/mapping-pipeline', 'report.tex'))</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> # self.pdf_latex = self.template.render(pipeline=self, metric=self.metric)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> template_dir = os.path.dirname(__file__) #'/usr/share/mapping-pipeline'</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;">- template_file = 'report.tex'</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;">+ template_file = '/usr/share/mapping-pipeline/report.tex'</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> loader = jinja2.FileSystemLoader(template_dir)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> env = jinja2.Environment(loader=loader)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> template = env.get_template(template_file)</span></pre>
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<li id="dab3de00a53f9de2b5f006a799a73a524a2a7cee">
<a href="https://salsa.debian.org/med-team/mapping-pipeline/compare/124837ebe731976a79e8a88e36a721dc4bd12894...362142266a0d580638bfbefa7c9652cf05760cf2#dab3de00a53f9de2b5f006a799a73a524a2a7cee"><strong>debian/patches/picard.patch</strong></a>
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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/mapping.py</span></span>
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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/mapping.py</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -390,7 +390,7 @@ class MAPPING:</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> self.args.reference = files</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"> def _valid_picard(self, f):</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if os.path.isfile(os.path.join(os.path.realpath(f), 'picard.jar')):</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if os.path.isfile(os.path.join('/usr/share/java', 'picard.jar')):</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> return f</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> raise argparse.ArgumentTypeError('Cannot find picard.jar in folder {}'.format(os.path.realpath(f)))</span></pre>
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<a href="https://salsa.debian.org/med-team/mapping-pipeline/compare/124837ebe731976a79e8a88e36a721dc4bd12894...362142266a0d580638bfbefa7c9652cf05760cf2#e246f69e945a7c2e9a8e25cfacfcac7714c92b69"><strong>debian/patches/python3.patch</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">@@ -7,14 +7,12 @@ Description: This script should not be called directly</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/metrics.py</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/metrics.py</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,<span class="idiff left right">6 +1,4</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,<span class="idiff left right">5 +1,3</span> @@</span></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;">-#!/usr/bin/env python</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;">-</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;">-import custom_logger as log</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;">+from . import custom_logger as log</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> import custom_logger as log</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> import matplotlib</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> matplotlib.use('Agg')</span>
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18
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -120,7 +118,7 @@ class METRICS:</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> self.reads_per_quality_result.append([os.path.realpath(os.path.join(self.output, 'reads_per_quality_{}.pdf'.format(valid_filename(reference)))), reference.replace('_','\_')])</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> fig, ax = plt.subplots( nrows=1, ncols=1 ) # create figure & 1 axis</span>
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<a href="https://salsa.debian.org/med-team/mapping-pipeline/compare/124837ebe731976a79e8a88e36a721dc4bd12894...362142266a0d580638bfbefa7c9652cf05760cf2#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">python3.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">config.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">picard.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">path_to_report.tex.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/mapping-pipeline/compare/124837ebe731976a79e8a88e36a721dc4bd12894...362142266a0d580638bfbefa7c9652cf05760cf2#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">@@ -10,5 +10,5 @@ override_dh_fixperms:</td>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> find debian -name "*.tex" -exec chmod -x \{\} \;</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> find debian -name "*.json" -exec chmod -x \{\} \;</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> for py in `find debian -name "*.py"` ; do \</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> if ! head -n 1 $$py | grep -q '^#!<span class="idiff left right">/usr/bin/</span>python' ; then chmod -x $$py ; fi ; \</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> if ! head -n 1 $$py | grep -q '^#!<span class="idiff left right"> */usr/bin/.*</span>python' ; then chmod -x $$py ; fi ; \</span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> done</span></pre>
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