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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>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/-/commit/ffdc327858cbedf8bd9d3d7f1a777cdebac537e7">ffdc3278</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-05-07T23:55:11+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Always use our Rscript.
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
debian/README.source
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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="#d6ced92a32c1cb2bcf2424c7b3ec4d1a699889c1">
<span class="new-file">
+
debian/patches/RscriptIsSystemVersion.patch
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</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/ffdc327858cbedf8bd9d3d7f1a777cdebac537e7#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</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">@@ -4,5 +4,9 @@ bcbio for Debian</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Please be aware that this package provides what upstream distributes</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">as bcbio-nextgen.</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">debian/patches/RscriptIsSystemVersion.patch:</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> This Debian package should always work with Debian's Rscript since</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> we have also installed our R modules with the system.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Sun, 11 Feb 2018 18:40:28 +0100</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/ffdc327858cbedf8bd9d3d7f1a777cdebac537e7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" 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">@@ -4,6 +4,7 @@ bcbio (1.2.8-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Removed now obsolete patch on abc collections</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Updated dependencies</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Point to system version of Rscript - always</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"> -- Steffen Moeller <moeller@debian.org> Fri, 07 May 2021 20:29:57 +0200</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/ffdc327858cbedf8bd9d3d7f1a777cdebac537e7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" 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">@@ -56,13 +56,15 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> pythonpy <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> rapmap <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> rna-star <!nocheck>,</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> r-<span class="idiff left right">other-wasabi</span> <!nocheck>,</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> r-<span class="idiff left right">base-core</span> <!nocheck>,</span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> r-bioc-htsfilter <!nocheck>,</span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> r-bioc-degreport <!nocheck>,</span>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> r-bioc-purecn <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> r-bioc-summarizedexperiment <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> r-cran-tidyverse <!nocheck>,</span>
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> r-bioc-titancna <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> r-bioc-tximport <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> r-other-wasabi <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> salmon <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> samblaster <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> samtools <!nocheck>,</span>
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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">@@ -182,6 +184,8 @@ Suggests: toil,</td>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="plaintext"> tophat2,</span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext"># found in source code but not exactly sure about its importance</span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="plaintext"> tophat-recondition,</span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"> r-bioc-summarizedexperiment,</span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> r-cran-tidyverse,</span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="plaintext"> r-other-wasabi</span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="plaintext">Description: toolkit for analysing high-throughput sequencing data</span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="plaintext"> This package installs the command line tools of the bcbio-nextgen</span>
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<li id="d6ced92a32c1cb2bcf2424c7b3ec4d1a699889c1">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/ffdc327858cbedf8bd9d3d7f1a777cdebac537e7#d6ced92a32c1cb2bcf2424c7b3ec4d1a699889c1"><strong>debian/patches/RscriptIsSystemVersion.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="p">Author: Steffen Moeller <moeller@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: With Debian we want to use _our_ R installation, while with the</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> typical conda-installation of bcbio this is the other way around. It is</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> important not to mix these up, hence this strict return of the sytem</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> version.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> This patch is not meant to be sent upstream.</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: bcbio/bcbio/utils.py</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</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;">--- bcbio.orig/bcbio/utils.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;">+++ bcbio/bcbio/utils.py</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">@@ -694,18 +694,11 @@</span> def dictapply(d, fn):</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> return d</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"> def Rscript_cmd(env="base"):</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;">- """Retrieve path to locally installed Rscript in the given env.</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;">+ """Original bcbio: Retrieve path to locally installed Rscript in the given env.</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> Prefers Rscript version installed via conda to a system version.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Debian: We use ours.</span></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"><span class="gd" style="color: #000; background-color: #fdd;">- if env == "base":</span></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;">- rscript = which(os.path.join(get_bcbio_bin(), "Rscript"))</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;">- else:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- conda_dir = get_conda_dir()</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rscript = os.path.join(conda_dir, "envs", env, "bin", "Rscript")</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if rscript:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return rscript</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return which("Rscript")</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return "/usr/bin/Rscript"</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> def R_sitelib(env="base"):</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> """Retrieve the R site-library installed with the bcbio installer for a given</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/ffdc327858cbedf8bd9d3d7f1a777cdebac537e7#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,3 +6,4 @@ pythonpaths.patch</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">hts_nim_tools.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">cnvkitPath.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">fixeFreetypePreload.patch</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">RscriptIsSystemVersion.patch</span></pre>
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