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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcbio">Debian Med / bcbio</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/9dfe1f4250c04d3343754630950a0698e2ed3e11">9dfe1f42</a></strong>
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<span>by Steffen Möller</span>
<i>at 2019-01-21T22:57:04Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed Python3 incompatibility
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<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/22a63cd0c73b96fb883956896e602494eb9d2719">22a63cd0</a></strong>
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<span>by Steffen Möller</span>
<i>at 2019-01-22T10:48:20Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Demoted seqcluster as 'recommended'
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<h4>4 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="#e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
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+
debian/patches/python3.patch
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debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bcbio/compare/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd...22a63cd0c73b96fb883956896e602494eb9d2719#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bcbio (1.1.2-2) 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"> * Found Python3 incompatbility. Upstream has it already.</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"> -- Steffen Moeller <moeller@debian.org> Mon, 21 Jan 2019 23:56:26 +0100</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">bcbio (1.1.2-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Initial release (Closes: #903386)</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bcbio/compare/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd...22a63cd0c73b96fb883956896e602494eb9d2719#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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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>
<td class="diff-line-num unfold js-unfold new_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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,8 +31,8 @@ Package: python3-bcbio</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> python3-seqcluster,</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> python3-tornado</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Recommends: python3-seqcluster</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Description: library for analysing high-throughput sequencing data</span>
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<td class="diff-line-num old_line" data-linenumber="37" 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="LC37" class="line" lang="plaintext"> This package installs the Python 3 libraries of the bcbio-nextgen</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> toolkit implementing best-practice pipelines for fully automated high</span>
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<li id="e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
<a href="https://salsa.debian.org/med-team/bcbio/compare/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd...22a63cd0c73b96fb883956896e602494eb9d2719#e246f69e945a7c2e9a8e25cfacfcac7714c92b69"><strong>debian/patches/python3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bcbio/bcbio/qc/contamination.py</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcbio.orig/bcbio/qc/contamination.py</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcbio/bcbio/qc/contamination.py</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -39,7 +39,7 @@ def _generate_estimates(bam_file, out_ba</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> cmd += _get_input_args(bam_file, data, out_base, background)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> do.run(cmd, "VerifyBamID contamination checks")</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except subprocess.CalledProcessError, msg:</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except subprocess.CalledProcessError as msg:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> def allowed_errors(l):</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> return (l.find("Insufficient Available markers") >= 0 or</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> l.find("No reads found in any of the regions") >= 0)</span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/compare/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd...22a63cd0c73b96fb883956896e602494eb9d2719#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></pre>
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