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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/gubbins">Debian Med / gubbins</a>
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<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/gubbins/commit/c62bd388f4e5ea7a28ff28bbb1cc8743bfdf1fbf">c62bd388</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-01-09T02:34:14+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixes
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#3a2470b33ad88916745979351435ccba0d2f1100">
debian/patches/gubbins_exe_in_usr_lib.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/gubbins/commit/c62bd388f4e5ea7a28ff28bbb1cc8743bfdf1fbf#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gubbins (2.4.0-2) 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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Fix run_gubbins wrapper (Sascha Steinbiss)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * raxml needed as default method at runtime - turned back into</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> hard dependency (suggested by Sascha)</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"> -- Steffen Moeller <moeller@debian.org> Thu, 09 Jan 2020 02:31:16 +0100</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">gubbins (2.4.0-1) 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/gubbins/commit/c62bd388f4e5ea7a28ff28bbb1cc8743bfdf1fbf#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -28,10 +28,10 @@ Architecture: any</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> python3</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">Recommends: iqtree,</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> fasttree,</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> raxml</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Recommends: iqtree,</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> fasttree</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Description: phylogenetic analysis of genome sequences</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> Gubbins supports rapid phylogenetic analysis of large samples of</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> recombinant bacterial whole genome sequences.</span>
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<li id="3a2470b33ad88916745979351435ccba0d2f1100">
<a href="https://salsa.debian.org/med-team/gubbins/commit/c62bd388f4e5ea7a28ff28bbb1cc8743bfdf1fbf#3a2470b33ad88916745979351435ccba0d2f1100"><strong>debian/patches/gubbins_exe_in_usr_lib.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">@@ -5,19 +5,6 @@ Description: gubbins executable prints that it is not intended for direct usage</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> it prints that it is intended to be called from run_gubbins. So it makes</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> sense to rather install it to /usr/lib/gubbins instead of /usr/bin.</span>
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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">Index: gubbins/python/gubbins/common.py</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- gubbins.orig/python/gubbins/common.py</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ gubbins/python/gubbins/common.py</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="p">@@ -48,7 +48,7 @@</span> def parse_and_run(input_args, program_de</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> printer = utils.VerbosePrinter(True, "\n")</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> # Check if the Gubbins C-program is available. If so, print a welcome message. Otherwise exit.</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gubbins_exec = 'gubbins'</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ gubbins_exec = '/usr/lib/gubbins/gubbins'</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> if utils.which(gubbins_exec) is None:</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> # Check if the Gubbins C-program is available in its source directory (for tests/Travis)</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> gubbins_bundled_exec = os.path.abspath(os.path.join(current_directory, '../src/gubbins'))</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff">Index: gubbins/src/main.c</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- gubbins.orig/src/main.c</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" 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>
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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">@@ -31,3 +18,15 @@ Index: gubbins/src/main.c</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> fprintf (stream, "Usage: %s [options] alignment_file\n", program_name);</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> fprintf (stream, "Version: %s\n", PACKAGE_VERSION);</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> fprintf (stream,</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gh" style="color: #999;">Index: gubbins/python/gubbins/common.py</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></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;">--- gubbins.orig/python/gubbins/common.py</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;">+++ gubbins/python/gubbins/common.py</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -48,6 +48,7 @@</span> def parse_and_run(input_args, program_de</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> printer = utils.VerbosePrinter(True, "\n")</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"> # Check if the Gubbins C-program is available. If so, print a welcome message. Otherwise exit.</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;">+ os.environ["PATH"] = os.environ["PATH"] + ":/usr/lib/gubbins/" </span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> gubbins_exec = 'gubbins'</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> if utils.which(gubbins_exec) is None:</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> # Check if the Gubbins C-program is available in its source directory (for tests/Travis)</span></pre>
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