<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en">
<head>
<meta content="text/html; charset=US-ASCII" http-equiv="Content-Type">
<title>
GitLab
</title>

<style data-premailer="ignore" type="text/css">
a { color: #1068bf; }
</style>


<style>img {
max-width: 100%; height: auto;
}
body {
font-size: 0.875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,0.01) 0 0 1px;
}
body {
font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Noto Sans", Ubuntu, Cantarell, "Helvetica Neue", sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji"; font-size: inherit;
}
</style>
</head>
<body style='font-size: inherit; -webkit-text-shadow: rgba(255,255,255,0.01) 0 0 1px; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Noto Sans", Ubuntu, Cantarell, "Helvetica Neue", sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji";'>
<div class="content">

<h3 style="margin-top: 20px; margin-bottom: 10px;">
Andreas Tille pushed to branch upstream at <a href="https://salsa.debian.org/med-team/gubbins">Debian Med / gubbins</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/gubbins/-/commit/c3ba1c5251fbd2065bb1217b791ddace027cce14">c3ba1c52</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2023-02-07T10:04:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>New upstream version 3.3</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#fe77d5d1439f26e353a42bbd38dece2467ff6558">
<span class="new-file">
+
.github/workflows/build.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="deleted-file">

.travis.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
</a>
</li>
<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
<span class="deleted-file">

Dockerfile
</span>
</a>
</li>
<li class="file-stats">
<a href="#acb1f594d797fb10fdb0aea6afb871238bbe1515">
<span class="deleted-file">

GubbinsManual_latest.docx
</span>
</a>
</li>
<li class="file-stats">
<a href="#d5b4de16d947214ec306bd57bed1bd23a939b5f9">
Makefile.am
</a>
</li>
<li class="file-stats">
<a href="#162af5feb7eb9e98ece9058301c1521b8b9abe0c">
<span class="new-file">
+
R/scripts/treeWAS_run.R
</span>
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
</a>
</li>
<li class="file-stats">
<a href="#f4919502f59714aa98c2d5c8a78855a31c295c88">
<span class="new-file">
+
codecov.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
</a>
</li>
<li class="file-stats">
<a href="#bafdb3502355421f7d2baba654f27b2d08fce881">
<span class="new-file">
+
docs/gubbins_manual.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#30718ade46220423b6d5ad6b521eeb516b2891ea">
<span class="new-file">
+
docs/gubbins_tutorial.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#0e58f3bf2a2e313bb7a4842b6591344656bf2702">
<span class="new-file">
+
docs/pmen3_output.png
</span>
</a>
</li>
<li class="file-stats">
<a href="#54c391de2500e0856c23737daf64f9d931569110">
<span class="new-file">
+
environment.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#3d35e3247e704d4e74897d7a3245ccac846b770a">
example_data/PMEN1/PMEN1.branch_base_reconstruction.embl
</a>
</li>
<li class="file-stats">
<a href="#13fba0710e25540245e0591ec21201d16cc6a9f4">
example_data/PMEN1/PMEN1.filtered_polymorphic_sites.fasta
</a>
</li>
<li class="file-stats">
<a href="#0da7659dea4e148fc353d12febbfabdb30007232">
example_data/PMEN1/PMEN1.filtered_polymorphic_sites.phylip
</a>
</li>
<li class="file-stats">
<a href="#c772ecd6681d2df61a7a95beefca68a7e27575c7">
example_data/PMEN1/PMEN1.final_tree.tre
</a>
</li>
<li class="file-stats">
<a href="#e121cf5d76ffa1fb1d4f20047e44c5c01e0337d0">
<span class="new-file">
+
example_data/PMEN1/PMEN1.log
</span>
</a>
</li>
<li class="file-stats">
<a href="#ced6261f98f71aa6cc2e5f8279477d9a47e6116e">
<span class="new-file">
+
example_data/PMEN1/PMEN1.node_labelled.final_tree.tre
</span>
</a>
</li>
<li class="file-stats">
<a href="#437d84f52329d285b0b945d54ad814565dd474d4">
<span class="deleted-file">

example_data/PMEN1/PMEN1.node_labelled.tre
</span>
</a>
</li>
<li class="file-stats">
<a href="#ebf6188e59deed9af6a07d44261a9ba6d63b49fe">
example_data/PMEN1/PMEN1.per_branch_statistics.csv
</a>
</li>
<li class="file-stats">
<a href="#b5eb744105f46a414d549a364d4804f15fb21b32">
example_data/PMEN1/PMEN1.recombination_predictions.embl
</a>
</li>
<li class="file-stats">
<a href="#345546cdf8e74513d5747de76ea63125d21168c7">
example_data/PMEN1/PMEN1.recombination_predictions.gff
</a>
</li>
<li class="file-stats">
<a href="#23896c96653badb4cf77f79c3dfd778a1e22755e">
example_data/PMEN1/PMEN1.summary_of_snp_distribution.vcf
</a>
</li>
<li class="file-stats">
<a href="#cfda74e40b454574a1bb47dd97ea9c9acd67dad5">
<span class="new-file">
+
example_data/PMEN1/PMEN1_output.png
</span>
</a>
</li>
<li class="file-stats">
<a href="#2c5ca9d9e1d8c40b66ed0d78a291a9ef83e64760">
example_data/PMEN1/README.md
</a>
</li>
<li class="file-stats">
<a href="#03de0cb2afd4ba9995834ce6b7ef1b8f828fa971">
example_data/ST239/README.md
</a>
</li>
<li class="file-stats">
<a href="#d5d9156fc7aa9a7e976e2f4d7e940bfef84e2e7f">
example_data/ST239/ST239.branch_base_reconstruction.embl
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: 0.875rem;">
The diff was not included because it is too large.
</h5>

</div>
<div class="footer" style="margin-top: 10px;">
<p style="font-size: small; color: #666;">

<br>
<a href="https://salsa.debian.org/med-team/gubbins/-/commit/c3ba1c5251fbd2065bb1217b791ddace027cce14">View it on GitLab</a>.
<br>
You're receiving this email because of your account on <a target="_blank" rel="noopener noreferrer" href="https://salsa.debian.org">salsa.debian.org</a>. <a href="https://salsa.debian.org/-/profile/notifications" target="_blank" rel="noopener noreferrer" class="mng-notif-link">Manage all notifications</a> · <a href="https://salsa.debian.org/help" target="_blank" rel="noopener noreferrer" class="help-link">Help</a>
<script type="application/ld+json">{"@context":"http://schema.org","@type":"EmailMessage","action":{"@type":"ViewAction","name":"View Commit","url":"https://salsa.debian.org/med-team/gubbins/-/commit/c3ba1c5251fbd2065bb1217b791ddace027cce14"}}</script>


</p>
</div>
</body>
</html>