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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/blends-team/med">Debian Blends Team / med</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/blends-team/med/-/commit/c17b641c9d622cd9f2da37c4ced4cfce93d20265">c17b641c</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-11T21:50:46+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Analyse package mentioned at https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716
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<h4>3 changed files:</h4>
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<a href="#1fa14af30ec5db2d2a24865610c71f2bfdbbd126">
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covid-19_doc/bio_covid-19_dependencies
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+
covid-19_doc/bio_covid-19_dependencies_query
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<a href="#6d072c2122e74d0aa0bfeb56f2e3fd56014c34b6">
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covid-19_doc/bio_covid-19_dependencies_result
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<h4>Changes:</h4>
<li id="1fa14af30ec5db2d2a24865610c71f2bfdbbd126">
<a href="https://salsa.debian.org/blends-team/med/-/commit/c17b641c9d622cd9f2da37c4ced4cfce93d20265#1fa14af30ec5db2d2a24865610c71f2bfdbbd126"><strong>covid-19_doc/bio_covid-19_dependencies</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># Packages column of https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">## resolved: "20 dependencies on R packages for pigx-rnaseq would need to go here"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## todo: 20 dependencies on R packages for pigx-scrnaseq would need to go here</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">## Fixme: pigx-rnaseq and pigx-scrnaseq are missing in this list</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></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">nextflow</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">snakemake</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">nf-core</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">abacas</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">allelecount</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">ascat</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">bcftools</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">bedtools</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">biopython</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">blast</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">bowtie2</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">busco</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">bustools</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">bwa</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">cat</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">centrifuge</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">changeo</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">cutadapt</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">diamond</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">deeptools</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">drop-seq-tools</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">fastp</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">fastqc</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">filtlong</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">freebayes</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">gatk</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">graphmap2</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">guppy</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">htslib</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">htseq</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">ivar</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">java</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">kallisto</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">kraken2</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">krona</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">lumpy</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">manta</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">megahit</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">metabat</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">minia</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">minimap2</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">multiqc</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">muscle</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">nanolyse</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">nanoplot</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">numpy</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">pandas</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">parallel-fastq-dump</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">picard</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">porechop</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">presto</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">prodigal</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">pycoqc</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">python</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">qcat</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">qualimap</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">quast</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">r-cran-alakazam</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">r-cran-ggplot2</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">r-cran-rmarkdown</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">r-cran-shazam</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">r-cran-tigger</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">r-cran-locfit</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">r-bioc-deseq2</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">r-bioc-tximport</span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">r-cran-data.table</span>
</pre>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">r-cran-rlang</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">r-cran-ggrepel</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">r-cran-dt</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">r-cran-pheatmap</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">r-cran-corrplot</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">r-cran-reshape2</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">r-cran-plotly</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">r-cran-scales</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">r-cran-crosstalk</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">r-cran-gprofiler</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">r-bioc-summarizedexperiment</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">r-bioc-rtracklayer</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">r-cran-rjson</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">salmon</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">samtools</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">snpeff</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">snpsift</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">spades</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">sra-toolkit</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">rna-star</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">strelka</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">tiddit</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">trim-galore</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">unicycler</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">varscan2</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">vcftools</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">vep</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">vg</span></pre>
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<a href="https://salsa.debian.org/blends-team/med/-/commit/c17b641c9d622cd9f2da37c4ced4cfce93d20265#8a0c01883456a1514ce9078deb9a9cd201172df4"><strong>covid-19_doc/bio_covid-19_dependencies_query</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="p">#</span><span class="c1" style="color: #998; font-style: italic;">!/bin/sh</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"><span class="p">#</span> <span class="n" style="color: #333;">query</span> <span class="n" style="color: #333;">packages</span> <span class="n" style="color: #333;">mentioned</span> <span class="n" style="color: #333;">at</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"><span class="p">#</span> <span class="n" style="color: #333;">Packages</span> <span class="n" style="color: #333;">column</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">docs</span><span class="p">.</span><span class="n" style="color: #333;">google</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">spreadsheets</span><span class="p">/</span><span class="n" style="color: #333;">d</span><span class="p">/</span><span class="m" style="color: #099;">1</span><span class="n" style="color: #333;">tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM</span><span class="p">/</span><span class="n" style="color: #333;">edit</span><span class="p">?</span><span class="n" style="color: #333;">ts</span><span class="p">=</span><span class="m" style="color: #099;">5</span><span class="n" style="color: #333;">eb957ba</span><span class="p">#</span><span class="n" style="color: #333;">gid</span><span class="p">=</span><span class="m" style="color: #099;">543782716</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"><span class="p">#</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">usage</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">cat</span> <span class="p">>/</span><span class="n" style="color: #333;">dev</span><span class="p">/</span><span class="n" style="color: #333;">stderr</span> <span class="p"><<</span><span class="n" style="color: #333;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="n" style="color: #333;">Usage</span><span class="p">:</span> <span class="p">$</span><span class="m" style="color: #099;">0</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"> <span class="p">-</span><span class="n" style="color: #333;">h</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">help</span> <span class="n" style="color: #333;">screen</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="p">-</span><span class="n" style="color: #333;">m</span> <span class="n" style="color: #333;">forcing</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">mirror</span> <span class="n" style="color: #333;">over</span> <span class="n" style="color: #333;">local</span> <span class="n" style="color: #333;">one</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"> <span class="n" style="color: #333;">Query</span> <span class="n" style="color: #333;">UDD</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">packages</span> <span class="n" style="color: #333;">belonging</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">task</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">specified</span> <span class="n" style="color: #333;">blend</span><span class="p">.</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">sorted</span> <span class="n" style="color: #333;">according</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">usage</span> <span class="n" style="color: #333;">statistics</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">contains</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"> <span class="n" style="color: #333;">information</span> <span class="n" style="color: #333;">about</span> <span class="n" style="color: #333;">existence</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">autopkgtest</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">well</span> <span class="n" style="color: #333;">whether</span> <span class="n" style="color: #333;">the</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"> <span class="n" style="color: #333;">interface</span> <span class="n" style="color: #333;">might</span> <span class="n" style="color: #333;">require</span> <span class="n" style="color: #333;">X11</span> <span class="k" style="font-weight: 600;">or</span> <span class="k" style="font-weight: 600;">not</span><span class="p">.</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel"><span class="n" style="color: #333;">EOT</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="mosel"><span class="p">}</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="mosel"><span class="k" style="font-weight: 600;">if</span> <span class="p">[</span> <span class="c1" style="color: #998; font-style: italic;">! $(which psql) ] ; then</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="mosel"> <span class="n" style="color: #333;">cat</span> <span class="p"><<</span><span class="n" style="color: #333;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="mosel"><span class="n" style="color: #333;">No</span> <span class="n" style="color: #333;">PostgreSQL</span> <span class="n" style="color: #333;">client</span> <span class="n" style="color: #333;">providing</span> <span class="p">/</span><span class="n" style="color: #333;">usr</span><span class="p">/</span><span class="n" style="color: #333;">bin</span><span class="p">/</span><span class="n" style="color: #333;">psql</span> <span class="n" style="color: #333;">installed</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="mosel"><span class="n" style="color: #333;">On</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">Debian</span> <span class="nf" style="color: #900; font-weight: 600;">system</span> <span class="n" style="color: #333;">please</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="mosel"> <span class="n" style="color: #333;">sudo</span> <span class="n" style="color: #333;">apt</span><span class="p">-</span><span class="n" style="color: #333;">get</span> <span class="n" style="color: #333;">install</span> <span class="n" style="color: #333;">postgresql</span><span class="p">-</span><span class="n" style="color: #333;">client</span><span class="p">-</span><span class="n" style="color: #333;">common</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="mosel"><span class="n" style="color: #333;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">exit</span> <span class="m" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"><span class="n" style="color: #333;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="mosel"><span class="n" style="color: #333;">SERVICE</span><span class="p">=</span><span class="s2" style="color: #d14;">"service=udd"</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="mosel"><span class="p">#</span><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">local</span> <span class="n" style="color: #333;">UDD</span> <span class="n" style="color: #333;">clone</span> <span class="n" style="color: #333;">just</span> <span class="n" style="color: #333;">use</span> <span class="n" style="color: #333;">this</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="mosel"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">psql</span> <span class="p">$</span><span class="n" style="color: #333;">PORT</span> <span class="p">-</span><span class="n" style="color: #333;">l</span> <span class="m" style="color: #099;">2</span><span class="p">>/</span><span class="n" style="color: #333;">dev</span><span class="p">/</span><span class="n" style="color: #333;">null</span> <span class="p">|</span> <span class="n" style="color: #333;">grep</span> <span class="p">-</span><span class="n" style="color: #333;">qw</span> <span class="n" style="color: #333;">udd</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="mosel"> <span class="n" style="color: #333;">SERVICE</span><span class="p">=</span><span class="n" style="color: #333;">udd</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="mosel"><span class="n" style="color: #333;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="mosel"><span class="p">#</span> <span class="n" style="color: #333;">Check</span> <span class="n" style="color: #333;">UDD</span> <span class="n" style="color: #333;">connection</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel"><span class="k" style="font-weight: 600;">if</span> <span class="c1" style="color: #998; font-style: italic;">! psql $PORT $SERVICE -c "" 2>/dev/null ; then</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel"> <span class="n" style="color: #333;">echo</span> <span class="s2" style="color: #d14;">"No local UDD found, use public mirror."</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="mosel"> <span class="n" style="color: #333;">export</span> <span class="n" style="color: #333;">PGPASSWORD</span><span class="p">=</span><span class="s2" style="color: #d14;">"public-udd-mirror"</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel"> <span class="n" style="color: #333;">SERVICE</span><span class="p">=</span><span class="s2" style="color: #d14;">"--host=public-udd-mirror.xvm.mit.edu --port=5432 --username=public-udd-mirror udd"</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel"><span class="n" style="color: #333;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel"><span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">getopts</span> <span class="s2" style="color: #d14;">"hjm"</span> <span class="n" style="color: #333;">o</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">case</span> <span class="s2" style="color: #d14;">"${o}"</span> <span class="k" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel"> <span class="n" style="color: #333;">h</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel"> <span class="n" style="color: #333;">usage</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">exit</span> <span class="m" style="color: #099;">0</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="mosel"> <span class="p">;;</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="mosel"> <span class="n" style="color: #333;">m</span><span class="p">)</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel"> <span class="n" style="color: #333;">export</span> <span class="n" style="color: #333;">PGPASSWORD</span><span class="p">=</span><span class="s2" style="color: #d14;">"public-udd-mirror"</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel"> <span class="n" style="color: #333;">SERVICE</span><span class="p">=</span><span class="s2" style="color: #d14;">"--host=public-udd-mirror.xvm.mit.edu --port=5432 --username=public-udd-mirror udd"</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel"> <span class="p">;;</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="mosel"> <span class="p">*)</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"> <span class="n" style="color: #333;">usage</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">exit</span> <span class="m" style="color: #099;">1</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel"> <span class="p">;;</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="mosel"> <span class="n" style="color: #333;">esac</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="mosel"><span class="n" style="color: #333;">done</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="mosel"></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="mosel"><span class="n" style="color: #333;">output</span><span class="p">=</span><span class="s2" style="color: #d14;">"bio_covid-19_dependencies_result"</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="mosel"></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="mosel"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">psql</span><span class="p">-</span><span class="k" style="font-weight: 600;">public</span><span class="p">-</span><span class="n" style="color: #333;">udd</span> <span class="p">>/</span><span class="n" style="color: #333;">dev</span><span class="p">/</span><span class="n" style="color: #333;">null</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="mosel"> <span class="n" style="color: #333;">RUNPSQL</span><span class="p">=</span><span class="n" style="color: #333;">psql</span><span class="p">-</span><span class="k" style="font-weight: 600;">public</span><span class="p">-</span><span class="n" style="color: #333;">udd</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="mosel"><span class="k" style="font-weight: 600;">else</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="mosel"> <span class="n" style="color: #333;">RUNPSQL</span><span class="p">=</span><span class="s2" style="color: #d14;">"psql $SERVICE"</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="mosel"><span class="n" style="color: #333;">fi</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="mosel"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="mosel"><span class="n" style="color: #333;">echo</span> <span class="s2" style="color: #d14;">"Last-Update: `date -R`"</span> <span class="p">></span> <span class="s2" style="color: #d14;">"$output"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="68" 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">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="mosel"><span class="n" style="color: #333;">echo</span> <span class="p">>></span> <span class="s2" style="color: #d14;">"$output"</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="mosel"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="mosel"><span class="p">$</span><span class="n" style="color: #333;">RUNPSQL</span> <span class="p">>></span><span class="s2" style="color: #d14;">"$output"</span> <span class="p"><<</span><span class="n" style="color: #333;">EOT</span></span>
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<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="mosel"><span class="n" style="color: #333;">SELECT</span> <span class="k" style="font-weight: 600;">package</span><span class="p">,</span> <span class="n" style="color: #333;">string_agg</span><span class="p">(</span><span class="n" style="color: #333;">architecture</span><span class="p">,</span> <span class="s1" style="color: #d14;">','</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">architectures</span> <span class="k" style="font-weight: 600;">FROM</span> <span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="72" 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">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="mosel"> <span class="n" style="color: #333;">SELECT</span> <span class="n" style="color: #333;">DISTINCT</span> <span class="k" style="font-weight: 600;">package</span><span class="p">,</span> <span class="n" style="color: #333;">architecture</span> <span class="k" style="font-weight: 600;">FROM</span> <span class="n" style="color: #333;">packages</span> <span class="n" style="color: #333;">WHERE</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="mosel"> <span class="n" style="color: #333;">architecture</span> <span class="k" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s1" style="color: #d14;">'all'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'amd64'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'arm64'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'ppc64el'</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">and</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">package</span> <span class="k" style="font-weight: 600;">in</span> <span class="p">(</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="mosel"><span class="s1" style="color: #d14;">'nextflow'</span><span class="p">,</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="mosel"><span class="s1" style="color: #d14;">'snakemake'</span><span class="p">,</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="mosel"><span class="s1" style="color: #d14;">'nf-core'</span><span class="p">,</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="mosel"><span class="s1" style="color: #d14;">'abacas'</span><span class="p">,</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="mosel"><span class="s1" style="color: #d14;">'allelecount'</span><span class="p">,</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="mosel"><span class="s1" style="color: #d14;">'ascat'</span><span class="p">,</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="mosel"><span class="s1" style="color: #d14;">'bcftools'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="mosel"><span class="s1" style="color: #d14;">'bedtools'</span><span class="p">,</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="mosel"><span class="s1" style="color: #d14;">'biopython'</span><span class="p">,</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;">'blast'</span><span class="p">,</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="mosel"><span class="s1" style="color: #d14;">'bowtie2'</span><span class="p">,</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="mosel"><span class="s1" style="color: #d14;">'busco'</span><span class="p">,</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="mosel"><span class="s1" style="color: #d14;">'bustools'</span><span class="p">,</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="mosel"><span class="s1" style="color: #d14;">'bwa'</span><span class="p">,</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="mosel"><span class="s1" style="color: #d14;">'cat'</span><span class="p">,</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="mosel"><span class="s1" style="color: #d14;">'centrifuge'</span><span class="p">,</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="mosel"><span class="s1" style="color: #d14;">'changeo'</span><span class="p">,</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="mosel"><span class="s1" style="color: #d14;">'cutadapt'</span><span class="p">,</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="mosel"><span class="s1" style="color: #d14;">'diamond'</span><span class="p">,</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="mosel"><span class="s1" style="color: #d14;">'deeptools'</span><span class="p">,</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="mosel"><span class="s1" style="color: #d14;">'drop-seq-tools'</span><span class="p">,</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="mosel"><span class="s1" style="color: #d14;">'fastp'</span><span class="p">,</span></span>
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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;">'fastqc'</span><span class="p">,</span></span>
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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;">'filtlong'</span><span class="p">,</span></span>
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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;">'freebayes'</span><span class="p">,</span></span>
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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;">'gatk'</span><span class="p">,</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="mosel"><span class="s1" style="color: #d14;">'graphmap2'</span><span class="p">,</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="mosel"><span class="s1" style="color: #d14;">'guppy'</span><span class="p">,</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="mosel"><span class="s1" style="color: #d14;">'htslib'</span><span class="p">,</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="mosel"><span class="s1" style="color: #d14;">'htseq'</span><span class="p">,</span></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;">'ivar'</span><span class="p">,</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="mosel"><span class="s1" style="color: #d14;">'java'</span><span class="p">,</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;">'kallisto'</span><span class="p">,</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="mosel"><span class="s1" style="color: #d14;">'kraken2'</span><span class="p">,</span></span>
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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;">'krona'</span><span class="p">,</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="mosel"><span class="s1" style="color: #d14;">'lumpy'</span><span class="p">,</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="mosel"><span class="s1" style="color: #d14;">'manta'</span><span class="p">,</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="mosel"><span class="s1" style="color: #d14;">'megahit'</span><span class="p">,</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="mosel"><span class="s1" style="color: #d14;">'metabat'</span><span class="p">,</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="mosel"><span class="s1" style="color: #d14;">'minia'</span><span class="p">,</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="mosel"><span class="s1" style="color: #d14;">'minimap2'</span><span class="p">,</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="mosel"><span class="s1" style="color: #d14;">'multiqc'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="mosel"><span class="s1" style="color: #d14;">'muscle'</span><span class="p">,</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="mosel"><span class="s1" style="color: #d14;">'nanolyse'</span><span class="p">,</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="mosel"><span class="s1" style="color: #d14;">'nanoplot'</span><span class="p">,</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="mosel"><span class="s1" style="color: #d14;">'numpy'</span><span class="p">,</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="mosel"><span class="s1" style="color: #d14;">'pandas'</span><span class="p">,</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="mosel"><span class="s1" style="color: #d14;">'parallel-fastq-dump'</span><span class="p">,</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="mosel"><span class="s1" style="color: #d14;">'picard'</span><span class="p">,</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="mosel"><span class="s1" style="color: #d14;">'porechop'</span><span class="p">,</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="mosel"><span class="s1" style="color: #d14;">'presto'</span><span class="p">,</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="mosel"><span class="s1" style="color: #d14;">'prodigal'</span><span class="p">,</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="mosel"><span class="s1" style="color: #d14;">'pycoqc'</span><span class="p">,</span></span>
</pre>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="mosel"><span class="s1" style="color: #d14;">'qcat'</span><span class="p">,</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="mosel"><span class="s1" style="color: #d14;">'qualimap'</span><span class="p">,</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="mosel"><span class="s1" style="color: #d14;">'quast'</span><span class="p">,</span></span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-cran-alakazam'</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-cran-ggplot2'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" 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">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-cran-rmarkdown'</span><span class="p">,</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">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-cran-shazam'</span><span class="p">,</span></span>
</pre>
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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;">'r-cran-tigger'</span><span class="p">,</span></span>
</pre>
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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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-cran-locfit'</span><span class="p">,</span></span>
</pre>
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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;">'r-bioc-deseq2'</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="138" 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">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-bioc-tximport'</span><span class="p">,</span></span>
</pre>
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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 class="s1" style="color: #d14;">'r-cran-data.table'</span><span class="p">,</span></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-cran-rlang'</span><span class="p">,</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-cran-ggrepel'</span><span class="p">,</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;">'r-cran-dt'</span><span class="p">,</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-cran-pheatmap'</span><span class="p">,</span></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-cran-corrplot'</span><span class="p">,</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;">'r-cran-reshape2'</span><span class="p">,</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;">'r-cran-plotly'</span><span class="p">,</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-cran-scales'</span><span class="p">,</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-cran-crosstalk'</span><span class="p">,</span></span>
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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;">'r-cran-gprofiler'</span><span class="p">,</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-bioc-summarizedexperiment'</span><span class="p">,</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-bioc-rtracklayer'</span><span class="p">,</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="mosel"><span class="s1" style="color: #d14;">'r-cran-rjson'</span><span class="p">,</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="mosel"><span class="s1" style="color: #d14;">'salmon'</span><span class="p">,</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="mosel"><span class="s1" style="color: #d14;">'samtools'</span><span class="p">,</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="mosel"><span class="s1" style="color: #d14;">'snpeff'</span><span class="p">,</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="mosel"><span class="s1" style="color: #d14;">'snpsift'</span><span class="p">,</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="mosel"><span class="s1" style="color: #d14;">'spades'</span><span class="p">,</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="mosel"><span class="s1" style="color: #d14;">'sra-toolkit'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="mosel"><span class="s1" style="color: #d14;">'rna-star'</span><span class="p">,</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="mosel"><span class="s1" style="color: #d14;">'strelka'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="mosel"><span class="s1" style="color: #d14;">'tiddit'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="mosel"><span class="s1" style="color: #d14;">'trim-galore'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="mosel"><span class="s1" style="color: #d14;">'unicycler'</span><span class="p">,</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="mosel"><span class="s1" style="color: #d14;">'varscan2'</span><span class="p">,</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="mosel"><span class="s1" style="color: #d14;">'vcftools'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="mosel"><span class="s1" style="color: #d14;">'vep'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="mosel"><span class="s1" style="color: #d14;">'vg'</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="mosel"><span class="p">)</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="mosel"> <span class="n" style="color: #333;">ORDER</span> <span class="n" style="color: #333;">BY</span> <span class="k" style="font-weight: 600;">package</span><span class="p">,</span> <span class="n" style="color: #333;">architecture</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="mosel"><span class="p">)</span> <span class="n" style="color: #333;">tmp</span> <span class="n" style="color: #333;">GROUP</span> <span class="n" style="color: #333;">by</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">ORDER</span> <span class="n" style="color: #333;">BY</span> <span class="k" style="font-weight: 600;">package</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="mosel"> <span class="p">;</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="mosel"><span class="n" style="color: #333;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/blends-team/med/-/commit/c17b641c9d622cd9f2da37c4ced4cfce93d20265#6d072c2122e74d0aa0bfeb56f2e3fd56014c34b6"><strong>covid-19_doc/bio_covid-19_dependencies_result</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">Last</span><span class="p">-</span><span class="n" style="color: #333;">Update</span><span class="p">:</span> <span class="n" style="color: #333;">Mon</span><span class="p">,</span> <span class="m" style="color: #099;">11</span> <span class="n" style="color: #333;">May</span> <span class="m" style="color: #099;">2020</span> <span class="m" style="color: #099;">21</span><span class="p">:</span><span class="m" style="color: #099;">48</span><span class="p">:</span><span class="m" style="color: #099;">13</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">package</span> <span class="p">|</span> <span class="n" style="color: #333;">architectures</span> </span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"><span class="p">-----------------------------+-------------------------</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="n" style="color: #333;">abacas</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="n" style="color: #333;">bcftools</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"> <span class="n" style="color: #333;">bedtools</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"> <span class="n" style="color: #333;">blast</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"> <span class="n" style="color: #333;">bowtie2</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="n" style="color: #333;">bustools</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"> <span class="n" style="color: #333;">bwa</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"> <span class="n" style="color: #333;">centrifuge</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"> <span class="n" style="color: #333;">changeo</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"> <span class="n" style="color: #333;">cutadapt</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"> <span class="n" style="color: #333;">diamond</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"> <span class="n" style="color: #333;">fastp</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel"> <span class="n" style="color: #333;">fastqc</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="mosel"> <span class="n" style="color: #333;">freebayes</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="mosel"> <span class="n" style="color: #333;">kallisto</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="mosel"> <span class="n" style="color: #333;">kraken2</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="mosel"> <span class="n" style="color: #333;">minia</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="mosel"> <span class="n" style="color: #333;">minimap2</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="mosel"> <span class="n" style="color: #333;">multiqc</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="mosel"> <span class="n" style="color: #333;">muscle</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="mosel"> <span class="n" style="color: #333;">picard</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="mosel"> <span class="n" style="color: #333;">porechop</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"> <span class="n" style="color: #333;">prodigal</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="mosel"> <span class="n" style="color: #333;">pycoqc</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="mosel"> <span class="n" style="color: #333;">qcat</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">bioc</span><span class="p">-</span><span class="n" style="color: #333;">deseq2</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">bioc</span><span class="p">-</span><span class="n" style="color: #333;">rtracklayer</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">bioc</span><span class="p">-</span><span class="n" style="color: #333;">summarizedexperiment</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">bioc</span><span class="p">-</span><span class="n" style="color: #333;">tximport</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">alakazam</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">corrplot</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">crosstalk</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" 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">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">table</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">dt</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">ggplot2</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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<td class="diff-line-num new new_line" data-linenumber="40" 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">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">ggrepel</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">gprofiler</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">locfit</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">pheatmap</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">plotly</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="45" 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">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">reshape2</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span><span class="p">,</span><span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">rjson</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">rlang</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">rmarkdown</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">scales</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span><span class="p">,</span><span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">shazam</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel"> <span class="n" style="color: #333;">r</span><span class="p">-</span><span class="n" style="color: #333;">cran</span><span class="p">-</span><span class="n" style="color: #333;">tigger</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="mosel"> <span class="n" style="color: #333;">rna</span><span class="p">-</span><span class="n" style="color: #333;">star</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"> <span class="n" style="color: #333;">salmon</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span></span>
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<td class="diff-line-num new new_line" data-linenumber="54" 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">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel"> <span class="n" style="color: #333;">samtools</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel"> <span class="n" style="color: #333;">snakemake</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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<td class="diff-line-num new new_line" data-linenumber="56" 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">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="mosel"> <span class="n" style="color: #333;">spades</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span></span>
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<td class="diff-line-num new new_line" data-linenumber="57" 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">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="mosel"> <span class="n" style="color: #333;">sra</span><span class="p">-</span><span class="n" style="color: #333;">toolkit</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="mosel"> <span class="nf" style="color: #900; font-weight: 600;">trim</span><span class="p">-</span><span class="n" style="color: #333;">galore</span> <span class="p">|</span> <span class="n" style="color: #333;">all</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="mosel"> <span class="n" style="color: #333;">unicycler</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="mosel"> <span class="n" style="color: #333;">vcftools</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span><span class="p">,</span><span class="n" style="color: #333;">arm64</span><span class="p">,</span><span class="n" style="color: #333;">ppc64el</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="mosel"> <span class="n" style="color: #333;">vg</span> <span class="p">|</span> <span class="n" style="color: #333;">amd64</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="mosel"><span class="p">(</span><span class="m" style="color: #099;">57</span> <span class="n" style="color: #333;">Zeilen</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="mosel"></span></pre>
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