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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/sepp">Debian Med / sepp</a>
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<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/sepp/-/commit/6e143e1e7abc420c81418e63400c7f2679e62e9b">6e143e1e</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-07-22T21:58:28+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Proceed with pplacer available now
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
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<li class="file-stats">
<a href="#baf09939cda3fe56aa57fe83e167d8594afc7d6b">
debian/patches/setup.patch
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<li class="file-stats">
<a href="#0fb2ebdf1422ca07aa40555402a7793da21fdefa">
<span class="new-file">
+
debian/patches/use_debian_packaged_guppy_from_pplacer.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sepp/-/commit/6e143e1e7abc420c81418e63400c7f2679e62e9b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">sepp (4.3.10+dfsg-1) UNRELEASED; 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"> * Initial release (Closes: #<bug>)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Needs https://salsa.debian.org/med-team/pplacer</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sun, 24 May 2020 06:37:36 +0200</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/sepp/-/commit/6e143e1e7abc420c81418e63400c7f2679e62e9b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,10 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3,</span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> python3-setuptools</span>
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<td class="diff-line-num new old_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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<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="plaintext"> python3-setuptools,</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="plaintext"> pplacer,</span>
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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">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> hmmer</span>
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<td class="diff-line-num new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<td class="diff-line-num old_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">
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/sepp</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/sepp.git</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/sepp/-/commit/6e143e1e7abc420c81418e63400c7f2679e62e9b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">setup.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">use_debian_packaged_guppy_from_pplacer.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/sepp/-/commit/6e143e1e7abc420c81418e63400c7f2679e62e9b#baf09939cda3fe56aa57fe83e167d8594afc7d6b"><strong>debian/patches/setup.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: 2020-05-24 15:54:37 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Do not check existence of third party tools since these are</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> removed. We are using Debian packaged tools</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/setup.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/setup.py</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">@@ -38,9 +38,9 @@</span> def get_tools_dir(where):</span>
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<a href="https://salsa.debian.org/med-team/sepp/-/commit/6e143e1e7abc420c81418e63400c7f2679e62e9b#0fb2ebdf1422ca07aa40555402a7793da21fdefa"><strong>debian/patches/use_debian_packaged_guppy_from_pplacer.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, 22 Jul 2020 21:53:32 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Use Debian packaged guppy</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/sepp-package/run-sepp.sh</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/sepp-package/run-sepp.sh</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -146,7 +146,7 @@</span> cp $tmp/${name}_rename-json.py .</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> # we might want to split computation in two parts: a) obtaining placements and b) creation of an insertion tree.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> # If -n set to something, we stop after a) and leave it to the user to compute b) afterwards.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> if [ -z ${noTree+x} ]; then</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gbin=$( dirname `grep -A1 "pplacer" $DIR/sepp/.sepp/main.config |grep path|sed -e "s/^path=//g"` )</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;">+ gbin="/usr/bin/"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> $gbin/guppy tog ${name}_placement.json</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </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;">--- a/setup.py</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;">+++ b/setup.py</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -45,7 +45,7 @@</span> def get_tools_dir(where):</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </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"> def get_tool_name(tool, bits):</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if platform.system() == "Darwin" or not bits: # MAC doesn't have 32/64</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if platform.system() == "Darwin" or True: # Never add anything to tool name under Debian</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> return tool</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> is_64bits = sys.maxsize > 2**32</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> return "%s-%s" % (tool, "64" if is_64bits else "32")</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -81,7 +81,7 @@</span> class ConfigSepp(Command):</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> def copy_tool_to_lib(self, tool, where=None, bits=True):</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> shutil.copy2(</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.path.join(get_tools_dir(where), get_tool_name(tool, bits)),</span></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;">+ os.path.join("/usr/bin", get_tool_name(tool, bits)),</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> os.path.join(self.get_tools_dest(), tool))</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"> def initialize_options(self):</span></pre>
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