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Rationale

Set the default pipeline tool directory as well as the sequence tools-specific path

Changes

  • Make sure that the code can find bgzip both when executed directly through BgzipRunner as well as invoked as part of a larger shell command through SequencePipelineServiceImpl.sortROD()

@labkey-jeckels
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@bbimber FYI JBrowseTest started failing on TeamCity over the holiday break. I can't find a cause, but I also don't understand how it was finding bgzip when it was executing the longer shell command. I think it has to be something related to Gradle or TeamCity, and shouldn't impact your production usage, but feel free to take a look.

@bbimber
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bbimber commented Jan 7, 2025

hmm. I do not watch devel all that closely, so I didnt see this. I also dont understand why this would suddenly change.

in general, i'm perfectly fine if you want to kick these kinds of things back to me to take a first pass investigation, but thanks for following up on this one.

@labkey-jeckels labkey-jeckels merged commit 0728b90 into develop Jan 7, 2025
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@labkey-jeckels labkey-jeckels deleted the fb_publishHiddenFiles branch January 7, 2025 03:02
labkey-tchad added a commit that referenced this pull request Jan 9, 2025
bbimber added a commit that referenced this pull request Jun 16, 2025
* Stream JSON results to client

* Use ActionURL to build lucene queries

* Switch to ExportAction

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Co-authored-by: Sebastian Benjamin <sebastiancbenjamin@gmail.com>
Co-authored-by: bbimber <bbimber@gmail.com>
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4 participants