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Allow adding arbitrary config to refseq block #884

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merged 2 commits into from Jan 26, 2018

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erasche commented Apr 19, 2017

Just like bin/flatfile-to-json.pl, this change enables a --config flag on prepare-refseqs.pl which allows adding arbitrary JSON to the refseq when it is added.

This is needed because I've started adding the metadata blocks for faceted track selector and as part of a completely automated pipeline. My tool that's building the trackList.json needs to be adding metadata to the right reference sequence, and I don't want to have to look through and guess which refseq track it is supposed to be.

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erasche commented Jan 23, 2018

Anyone? I noticed this as a "bug" in my galaxy wrapper for jbrowse and after some debugging ended up back here :)

This is a pretty small / unobtrusive change and otherwise I have to manually process the json and that's really ugly.

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nathandunn commented Jan 23, 2018

@rbuels Do you want to test this? Otherwise I can take a look. The changes seem good to me.

@rbuels

This is a great idea! Just a couple more things that need to be done before it's good to go:

  1. There is already a --conf option for prepare-refseqs, could you change the name of this option to --trackConfig or something similar instead?
  2. Please add POD documentation for the new option to bin/prepare-refseqs.pl
@@ -64,6 +65,12 @@ sub run {
$self->{chunkSize} = $chunkSize;
}
for my $optname ( qw( config ) ) {

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rbuels Jan 23, 2018

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could you add an explanatory comment here?

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erasche commented Jan 24, 2018

Is this better @rbuels? Thanks for taking the time to look at it!

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rbuels approved these changes Jan 25, 2018

@rbuels rbuels added this to the 1.12.4 milestone Jan 25, 2018

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rbuels commented Jan 25, 2018

Looks good. I just need to get all the perl tests running again before merging this.

@rbuels rbuels merged commit c107d93 into GMOD:master Jan 26, 2018

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@erasche erasche deleted the erasche:prepare-refesqs-config branch Jan 29, 2018

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