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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/kraken2">Debian Med / kraken2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken2/commit/27b63b3565c65ff17fd5d0c257394afd10c51421">27b63b35</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-03-14T08:54:00Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt from kraken to kraken2
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#a5309cd7965acff1bb92c2441d2e35620d51749b">
debian/dirs
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<li class="file-stats">
<a href="#af5e13ec7db0b92fee10569b5904cd0fb8b966a6">
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+
debian/patches/fix_install.patch
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<li class="file-stats">
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+
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="a5309cd7965acff1bb92c2441d2e35620d51749b">
<a href="https://salsa.debian.org/med-team/kraken2/commit/27b63b3565c65ff17fd5d0c257394afd10c51421#a5309cd7965acff1bb92c2441d2e35620d51749b"><strong>debian/dirs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">usr/bin</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">usr/lib/kraken</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">usr/lib/kraken<span class="idiff left right">2</span></span></pre>
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<li id="af5e13ec7db0b92fee10569b5904cd0fb8b966a6">
<a href="https://salsa.debian.org/med-team/kraken2/commit/27b63b3565c65ff17fd5d0c257394afd10c51421#af5e13ec7db0b92fee10569b5904cd0fb8b966a6"><strong>debian/patches/fix_install.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Wed, 13 Mar 2019 15:46:40 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: The temporary dir where to move the files for packaging is</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> different from the final location. Hardcode the final location here.</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"><span class="gd" style="color: #000; background-color: #fdd;">--- a/install_kraken2.sh</span></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/install_kraken2.sh</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -31,7 +31,7 @@ for file in scripts/*</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> do</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> perl -pl -e 'BEGIN { while (@ARGV) { $_ = shift; ($k,$v) = split /=/, $_, 2; $H{$k} = $v } }'\</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> -e 's/#####=(\w+)=#####/$H{$1}/g' \</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "KRAKEN2_DIR=$KRAKEN2_DIR" "VERSION=$VERSION" \</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "KRAKEN2_DIR=/usr/lib/kraken2" "VERSION=$VERSION" \</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> < "$file" > "$KRAKEN2_DIR/$(basename $file)"</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> if [ -x "$file" ]</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> then</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/kraken2/commit/27b63b3565c65ff17fd5d0c257394afd10c51421#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fix_install.patch</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/kraken2/commit/27b63b3565c65ff17fd5d0c257394afd10c51421#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">@@ -2,24 +2,25 @@</td>
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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"># DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">export KRAKEN2_DIR=$(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)</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">%:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh $@ --sourcedirectory=src</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">override_dh_link:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> dh_link</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> for file in $(<span class="idiff left right">CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/kraken</span>* ; do \</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> for file in $(<span class="idiff left right">KRAKEN2_DIR)/</span>* ; do \</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> if ! echo $${file} | grep -q '\.pm$$' ; then \</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> ln -s ../lib/$(DEB_SOURCE)/`basename $${file}` $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/`basename $${file}` ; \</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> fi \</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> dh_auto_install -- KRAKEN<span class="idiff left right">_DIR=$(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE</span>)</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> ./install_kraken<span class="idiff left right">.sh /usr/lib/$(DEB_SOURCE) $(DEB_SOURCE</span>)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> dh_auto_install -- KRAKEN<span class="idiff left right">2_DIR=$(KRAKEN2_DIR</span>)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> ./install_kraken<span class="idiff left right">2.sh $(KRAKEN2_DIR</span>)</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> dh_install</span>
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