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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/kleborate">Debian Med / kleborate</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/-/commit/400a89869e403fbef583f45b220b1d9e3f1bd4de">400a8986</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-22T16:55:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add bigendian.patch: fixes ftbfs on s390x
This patch fixes ftbfs on s390x, and other big endian architectures,
by allowing kleborate to fall back to blastdb version 4 for its sample
files and at run time.
Closes: #994714
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/-/commit/0ec16e278b4808ef4664966afa4903b5a888daf6">0ec16e27</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-22T18:53:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/-/commit/e5ba7a3e433fde6a296d1f31b986a03d528458f6">e5ba7a3e</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-22T18:54:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/-/commit/4ea22ff2f5db0d26d18e31e64d99b0b57d4078df">4ea22ff2</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-22T18:54:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Apply multi-arch hints.
+ kleborate-examples: Add Multi-Arch: foreign.
Changes-By: apply-multiarch-hints
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/-/commit/f60fa3b6220790c1cca3b564f09beac7d441c0b5">f60fa3b6</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-22T19:07:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#6de1e386377830e522ceda5a14f6c6849941e30b">
<span class="new-file">
+
debian/patches/bigendian.patch
</span>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kleborate/-/compare/39fda303975c992d09f53c3a756189307494e61e...f60fa3b6220790c1cca3b564f09beac7d441c0b5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kleborate (2.1.0-2) unstable; 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"> * add bigendian.patch: fixes ftbfs on s390x. (Closes: #994714)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Apply multi-arch hints.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> + kleborate-examples: Add Multi-Arch: foreign.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> Wed, 22 Sep 2021 18:54:42 +0200</span>
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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">kleborate (2.1.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Team Upload.</span>
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<a href="https://salsa.debian.org/med-team/kleborate/-/compare/39fda303975c992d09f53c3a756189307494e61e...f60fa3b6220790c1cca3b564f09beac7d441c0b5#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" 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">@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> ncbi-blast+ <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> mash <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> kaptive <!nocheck></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/kleborate</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/kleborate.git</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: https://github.com/katholt/Kleborate</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,6 +45,7 @@ Package: kleborate-examples</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Recommends: kleborate</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Multi-Arch: foreign</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">Description: tool to screen Klebsiella genome assemblies (example data)</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> Kleborate is a tool to screen Klebsiella genome assemblies for:</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> .</span>
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<li id="6de1e386377830e522ceda5a14f6c6849941e30b">
<a href="https://salsa.debian.org/med-team/kleborate/-/compare/39fda303975c992d09f53c3a756189307494e61e...f60fa3b6220790c1cca3b564f09beac7d441c0b5#6de1e386377830e522ceda5a14f6c6849941e30b"><strong>debian/patches/bigendian.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fall back to generating blast db v4 on big endian systems</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Kleborate is not capable of decoding blast db v5 on all architectures, because</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> the underlying format of the storage is processor architecture dependent, for</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> the sake of performance, at the cost of interoperability. The v4 format, in</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> contrast, is plaintext, so remains suitable in such context. Many Thanks to</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> Aaron M. Ucko for the details!</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/994714</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">Last-Update: 2021-09-21</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</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;">--- kleborate.orig/kleborate/__main__.py</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;">+++ kleborate/kleborate/__main__.py</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -625,6 +625,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> def rebuild_blast_indices(data_dir):</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> for fasta in pathlib.Path(data_dir).glob('*.fasta'):</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> makeblastdb_cmd = ['makeblastdb', '-dbtype', 'nucl', '-in', str(fasta)]</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Use blastdb v4 format for big endian systems, since the v5 format is</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # processor architecture dependent, but not the v4.</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;">+ if sys.byteorder == 'big':</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ makeblastdb_cmd += ['-blastdb_version', '4']</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> with open(os.devnull, 'w') as devnull:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> subprocess.check_call(makeblastdb_cmd, stdout=devnull)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- kleborate.orig/kleborate/blastn.py</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ kleborate/kleborate/blastn.py</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -13,6 +13,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </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"><span class="gi" style="color: #000; background-color: #dfd;">+import sys</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> import subprocess</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> from .misc import reverse_complement</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -135,5 +136,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> def build_blast_database_if_needed(seqs):</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> if not os.path.exists(seqs + '.nin'):</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> with open(os.devnull, 'w') as devnull:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- subprocess.check_call('makeblastdb -dbtype nucl -in ' + seqs, stdout=devnull,</span></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;">- shell=True)</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if sys.byteorder == 'little':</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ subprocess.check_call('makeblastdb -dbtype nucl -in ' + seqs,</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ stdout=devnull,</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ shell=True)</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ subprocess.check_call('makeblastdb -dbtype nucl -in ' + seqs</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ + ' -blastdb_version 4',</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ stdout=devnull,</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ shell=True)</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- kleborate.orig/setup.py</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ kleborate/setup.py</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="p">@@ -40,6 +40,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> def build_blast_db(data_dir, fasta_filename, seq_type):</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> fasta_path = os.path.join(data_dir, fasta_filename)</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> makeblastdb_cmd = ['makeblastdb', '-dbtype', seq_type, '-in', fasta_path]</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Fall back to blastdb version 4 for big endian architectures, as kleborate</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;">+ # is not yet able to swap bytes appropriately with the new lmdb format of</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;">+ # the blastdb v5. Note that the content of the distributed data set is</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # thus now architecture dependent.</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;">+ if sys.byteorder == 'big':</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ makeblastdb_cmd += ['-blastdb_version', '4']</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> print(' ' + ' '.join(makeblastdb_cmd))</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> with open(os.devnull, 'w') as devnull:</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> subprocess.check_call(makeblastdb_cmd, stdout=devnull)</span></pre>
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<a href="https://salsa.debian.org/med-team/kleborate/-/compare/39fda303975c992d09f53c3a756189307494e61e...f60fa3b6220790c1cca3b564f09beac7d441c0b5#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">python3.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">use_debian_installed_kaptive.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">bigendian.patch</span></pre>
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