Unable to find Atropos - Githubissues

bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

https://bcbio-nextgen.readthedocs.io

MIT License

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Closed keenhl closed 5 years ago

keenhl commented 5 years ago

I have did a new install of bcbio with datatarget snrnaseq, and did a tools update bcbio_nextgen.py upgrade --tools

However, I get the following error. I can find atropos in the tools/bin directory.

bcbio.pipeline.config_utils.CmdNotFound: '_get_program_cmd' 'atropos' {} 'atropos'

Any thoughts about why bcbio is not finding Atropos?

Thanks.

roryk commented 5 years ago

Hi @keenhl,

You'll need to add your tool directory to your path, and it should pick up atropos that way.

roryk commented 5 years ago

Thanks, closing this as this should solve the problem!