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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:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/-/commit/50ace2d97dffa89c7175c39a1f0edf608f971443">50ace2d9</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-11-14T22:30:48+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cnvkit executable now found without further ado
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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="#9e881a213ebe50467b299d1baae6d44f7c2b1283">
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+
debian/patches/cnvkitPath.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/50ace2d97dffa89c7175c39a1f0edf608f971443#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bcbio (1.2.4-3) UNELEASED; 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"> * Compatibility with Python 3.9</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Rounded-up Debian experience</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> - Added runtime/testing build depdendencies</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> - Adjusted names of executables in Debian</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> + hts-nim-tools</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> + cnvkit</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"> -- Steffen Moeller <moeller@debian.org> Sat, 14 Nov 2020 22:29:00 +0100</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">bcbio (1.2.4-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/50ace2d97dffa89c7175c39a1f0edf608f971443#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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="33" 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">@@ -33,6 +33,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> grabix <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> hisat2 <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> hts-nim-tools <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> lumpy-sv <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> mosdepth <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> multiqc <!nocheck>,</span>
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<td class="diff-line-num new_line" data-linenumber="39" 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="LC39" class="line" lang="plaintext"> perl <!nocheck>,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" 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="96" 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">@@ -95,6 +96,7 @@ Depends: ${python3:Depends},</td>
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95
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"> python3-tornado</span>
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96
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">Recommends:</span>
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97
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"> cnvkit,</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> lumpy-sv,</span>
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98
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"> mosdepth,</span>
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99
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"> multiqc,</span>
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100
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> python3-arrow,</span>
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<li id="9e881a213ebe50467b299d1baae6d44f7c2b1283">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/50ace2d97dffa89c7175c39a1f0edf608f971443#9e881a213ebe50467b299d1baae6d44f7c2b1283"><strong>debian/patches/cnvkitPath.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bcbio/bcbio/structural/cnvkit.py</span></span>
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2
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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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3
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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/structural/cnvkit.py</span></span>
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4
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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/structural/cnvkit.py</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -162,7 +162,7 @@</span> def _run_cnvkit_population(items, backgr</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> out.extend(_associate_cnvkit_out(ckouts, [cur_input]))</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> return out</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </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;">-def _get_cmd(script_name="cnvkit.py"):</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+def _get_cmd(script_name="cnvkit"):</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> return os.path.join(os.path.dirname(os.path.realpath(sys.executable)), script_name)</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> def _prep_cmd(cmd, tx_out_file):</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -493,7 +493,7 @@</span> def _add_seg_to_output(out, data, enumer</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> out_file = "%s.seg" % os.path.splitext(out["cns"])[0]</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> if not utils.file_exists(out_file):</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> with file_transaction(data, out_file) as tx_out_file:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "export",</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit"), "export",</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> "seg"]</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> if enumerate_chroms:</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> cmd += ["--enumerate-chroms"]</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -542,7 +542,7 @@</span> def _add_variantcalls_to_output(out, dat</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> if not utils.file_exists(call_file):</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> with file_transaction(data, call_file) as tx_call_file:</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> filters = ["--filter", "cn"]</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "call"] + \</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit"), "call"] + \</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> filters + \</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> ["--ploidy", str(ploidy.get_ploidy([data])),</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> "-o", tx_call_file, out["cns"]]</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -563,7 +563,7 @@</span> def _add_variantcalls_to_output(out, dat</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> calls[outformat] = out_file</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> if not os.path.exists(out_file):</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> with file_transaction(data, out_file) as tx_out_file:</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "export",</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit"), "export",</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> outformat, "--sample-id", dd.get_sample_name(data),</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> "--ploidy", str(ploidy.get_ploidy([data])),</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> "-o", tx_out_file, call_file]</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="p">@@ -581,7 +581,7 @@</span> def _add_segmetrics_to_output(out, data)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> out_file = "%s-segmetrics.txt" % os.path.splitext(out["cns"])[0]</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> if not utils.file_exists(out_file):</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> with file_transaction(data, out_file) as tx_out_file:</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "segmetrics",</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit"), "segmetrics",</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> "--median", "--iqr", "--ci", "--pi",</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> "-s", out["cns"], "-o", tx_out_file, out["cnr"]]</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> # Use less fine grained bootstrapping intervals for whole genome runs</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="p">@@ -599,7 +599,7 @@</span> def _add_gainloss_to_output(out, data):</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> out_file = "%s-gainloss.txt" % os.path.splitext(out["cns"])[0]</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> if not utils.file_exists(out_file):</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> with file_transaction(data, out_file) as tx_out_file:</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "gainloss",</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit"), "gainloss",</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> "-s", out["cns"], "-o", tx_out_file, out["cnr"]]</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> gender = _get_batch_gender([data])</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> if gender:</span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/50ace2d97dffa89c7175c39a1f0edf608f971443#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -6,3 +6,4 @@ do_not_use_git.patch</td>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">pythonpaths.patch</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">hts_nim_tools.patch</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">collectionsAbc.patch</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">cnvkitPath.patch</span></pre>
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