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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>
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<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/ce7a2658d980cc9af0179214c46870202294c69b">ce7a2658</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2019-06-24T14:58:16Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">seqcluster keeps making trouble
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<h4>1 changed file:</h4>
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<a href="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
debian/TODO
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<h4>Changes:</h4>
<li id="d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<a href="https://salsa.debian.org/med-team/bcbio/commit/ce7a2658d980cc9af0179214c46870202294c69b#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</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">@@ -75,13 +75,36 @@ package seqcluster</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ./.travis.yml:- conda install --yes -c conda-forge -c bioconda memory_profiler openjdk pysam pybedtools pandas numpy biopython progressbar2 pyyaml bedtools samtools mirtop viennarna -q</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="mosel"><span class="s1" style="color: #d14;"> so, for some successful testing it seems like we need viennarna, still. That is not yet in the distribution. If truly dependending on it then bcbio ends up in contrib.</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="mosel"><span class="s1" style="color: #d14;"> seqcluster redistributes a "Free as in beer" graph library in its source tree at ./misc/js/amcharts.js that upstream accepts to be substituted with references to the online location in a CDN. Steffen will address that. Downside of it all: seqcluster needs to go to contrib.</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Additional requirements:</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="mosel"><span class="s1" style="color: #d14;"> python3-dateutils (not yet packaged)</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="mosel"><span class="s1" style="color: #d14;"> python3-pytz (not yet packaged)</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="mosel"><span class="s1" style="color: #d14;"> And there are R packages that should be recommended at least (from https://github.com/lpantano/seqcluster/blob/master/scripts/install_libraries.R)</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="mosel"><span class="s1" style="color: #d14;"> # We cover all CRAN packages</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="mosel"><span class="s1" style="color: #d14;"> # Most BioC packages are missing - even edgeR ? :</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="mosel"><span class="s1" style="color: #d14;"> r-bioc-edgeR - missing</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="mosel"><span class="s1" style="color: #d14;"> r-bioc-HTSFilter - missing</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="mosel"><span class="s1" style="color: #d14;"> r-bioc-DEGreport - missing</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="mosel"><span class="s1" style="color: #d14;"> # novel packages</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="mosel"><span class="s1" style="color: #d14;"> install.github("hbc/CHBUtils") - missing</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="mosel"><span class="s1" style="color: #d14;"> install.github("lpantano/isomiRs", "master") - missing</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="mosel"><span class="s1" style="color: #d14;"> install_github('</span><span class="n" style="color: #333;">rstudio</span><span class="p">/</span><span class="n" style="color: #333;">rmarkdown</span><span class="s1" style="color: #d14;">') -- this may be the same we have from CRAN - not checked</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="mosel"><span class="s1" style="color: #d14;">package viennarna</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/ViennaRNA/ViennaRNA</span></span>
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80
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/vienna-rna/blob/master/debian/changelog</span></span>
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81
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="mosel"><span class="s1" style="color: #d14;"> No idea about where exactly we stand with this.</span></span>
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82
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The package now has a custom license file - redistributable but non-free.</span></span>
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83
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed for testing seqcluster.</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Steffen revisits ViennaRNA</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Steffen revisits ViennaRNA, will update to new upstream version this weekend</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Does not compile - source tree seems incomplete (RNAfold_cmdl.c missing)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="mosel"><span class="s1" style="color: #d14;"> External dependencies json (in Debian, I think, can otherwise be deconfigured) and cthreadpool (not yet in Debian) need to be addressed</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="mosel"></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="mosel"><span class="s1" style="color: #d14;">package cthreadpool</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/Pithikos/C-Thread-Pool/blob/master/thpool.h</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed by ViennaRNA</span></span>
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85
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="mosel"></span>
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86
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="mosel"><span class="s1" style="color: #d14;">Packages presumed easy to package</span></span>
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87
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<td class="diff-line-num new_line" data-linenumber="110" 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">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="mosel"><span class="s1" style="color: #d14;">---------------------------------</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="107" 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="130" 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">@@ -107,6 +130,20 @@ Package MutliQC - in salsa</td>
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107
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/multiqc</span></span>
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108
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Steffen will address this one</span></span>
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109
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<td class="diff-line-num new_line" data-linenumber="132" 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="LC132" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="mosel"><span class="s1" style="color: #d14;">r-bioc-edgeR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="134" 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="LC134" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://tracker.debian.org/pkg/r-bioc-edger</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="mosel"><span class="s1" style="color: #d14;"> This was removed from buster in February - a bit of a bummer, I tend to think</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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="LC136" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/r-pkg-team/r-bioc-edger</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://bioconductor.org/packages/release/bioc/html/edgeR.html</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed by seqcluster</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" 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">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="mosel"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="mosel"><span class="s1" style="color: #d14;">r-bioc-HTSFilter</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://bioconductor.org/packages/release/bioc/html/HTSFilter.html</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed by seqcluster</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="mosel"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="mosel"><span class="s1" style="color: #d14;">r-bioc-DEGreport</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://bioconductor.org/packages/release/bioc/html/DEGreport.html</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed by seqcluster</span></span>
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110
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="mosel"></span>
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111
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="mosel"></span>
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112
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="mosel"><span class="s1" style="color: #d14;">Packages of importance for basic NGS workflows with motivation beyond bcbio</span></span>
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