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Add desktop specific plugin tutorial #3193

Merged
merged 2 commits into from Sep 16, 2022
Merged

Add desktop specific plugin tutorial #3193

merged 2 commits into from Sep 16, 2022

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carolinebridge-oicr
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adds tutorial doc for writing a desktop specific plugin

@cmdcolin can you give this a quick read

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codecov bot commented Sep 15, 2022

Codecov Report

Merging #3193 (c080ff8) into main (ebd548c) will not change coverage.
The diff coverage is n/a.

❗ Current head c080ff8 differs from pull request most recent head 5b0c4ad. Consider uploading reports for the commit 5b0c4ad to get more accurate results

@@           Coverage Diff           @@
##             main    #3193   +/-   ##
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  Coverage   59.48%   59.48%           
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  Files         671      671           
  Lines       28734    28734           
  Branches     6968     6968           
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  Hits        17092    17092           
  Misses      11320    11320           
  Partials      322      322           

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@cmdcolin
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cmdcolin commented Sep 15, 2022

this is a great idea. can you make it clear what the plugin does in the start e.g. it is ok to be specific like "this tutorial will demonstrate making a desktop-specific jbrowse plugin to run external tools like bcftools and tabix on a VCF file"

doing bcftools stuff could be very useful for a variety of use cases also, might be a starter for additional stuff. another useful task would actually be creating a bigwig file from a BAM/CRAM file. your choice if you wanna try it out

requires mosdepth, gunzip, and bedGraphToBigWig programs to be installed

the commands for that look a bit like this

mosdepth output input.bam -f reference.fa 
gunzip output.per-base.bed.gz
bedGraphToBigWig output.per-base.bed reference.fa.fai output.bw 

@cmdcolin
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may also be good to show tying into the "jobs manager" on desktop for longer running jobs

@carolinebridge-oicr
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may also be good to show tying into the "jobs manager" on desktop for longer running jobs

added a potential feature request for making this realistically usable by plugin devs

going ahead w merge as feedback has been implemented

@carolinebridge-oicr carolinebridge-oicr marked this pull request as ready for review September 16, 2022 20:20
@carolinebridge-oicr carolinebridge-oicr merged commit 022e5c2 into main Sep 16, 2022
@cmdcolin cmdcolin deleted the dtplugin branch September 19, 2022 15:45
@cmdcolin cmdcolin changed the title [update docs] add desktop specific plugin tutorial Add desktop specific plugin tutorial Oct 3, 2022
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2 participants