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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
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STAR-Fusion is missing IGV Reports (igv-reports) dependency #16877

Closed acesnik closed 5 years ago

acesnik commented 5 years ago

Just encountered another dependency error in STAR-Fusion when running with FusionInspector options. (https://github.com/bioconda/bioconda-recipes/issues/16759 was just fixed)

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/star-fusion/meta.yaml#L20

needs to have - igv-reports, too

Error from STAR-Fusion:

Traceback (most recent call last):
  File "/home/acesnik/miniconda3/envs/spritz/lib/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py", line 7, in <module>
    from igv_reports import datauri
ModuleNotFoundError: No module named 'igv_reports'
acesnik commented 5 years ago

Just to confirm, STAR-Fusion finished with FusionInspector after adding igv-reports to my conda environment.

acesnik commented 5 years ago

It looks like you may also want to add - requests based on the FusionInspector software requirements. I'm not sure if that's part of the base distribution.

acesnik commented 5 years ago

It looks like there's also an option to use Trinity to do reconstruction, so maybe including - trinity is also in order.

https://github.com/FusionInspector/FusionInspector/wiki/De-novo-reconstruction-of-fusion-transcripts

https://github.com/STAR-Fusion/STAR-Fusion/blob/5e26eee39fc59dd45e4a13403726790b14e9a6fc/STAR-Fusion#L215

micknudsen commented 5 years ago

I have had to pin igv-reports==0.2.1. Other versions on bioconda are >=0.9.0, and they seem to be incompatible with STAR-Fusion.

acesnik commented 5 years ago

I had success yesterday with igv-reports=0.9.4, so maybe the issue was fixed. :)

acesnik commented 5 years ago

By the way, the latest version of trinity failed for me, so I'd recommend using - trinity=2.9.4-0

micknudsen commented 5 years ago

Maybe you ran into this bug which existed for a rather short time?

https://github.com/bioconda/bioconda-recipes/pull/16873

micknudsen commented 5 years ago

@acesnik You are right. Now STAR-Fusion also works for me with igv-reports=0.9.4.

bgruening commented 5 years ago

Cool thanks for catching up!