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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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Conda installing bowtie-build 1.0.0 by default #132

Closed thalescherubino closed 9 months ago

thalescherubino commented 1 year ago

Hi!

I am using this new ShortStack version and I tried setting the environment using conda as recommended. The issue is that conda is setting an old bowtie-build version that does not allows the use of multiple threads (--threads). That way, running SortStack with multiple threads the run is faling quite early.

MikeAxtell commented 1 year ago

Sorry to hear that. It is highly likely to be an issue with your specific conda installation or configuration. I've just confirmed that the shortstack bioconda recipe is working as intended on my system; the latest bowtie and everything else are pulled.

Double-check that your conda executable was installed and configured per the instructions for bioconda http://bioconda.github.io. If not, reinstall and reconfigure your conda. Specifically this sounds to me like a channel config or channel priority issue. Or, a deeply complicated conda environment on your device that may need to be cleaned up / deleted / fresh installed. Take a look at the FAQ section of ShortStack's README as well.

You can also manually install bowtie (and all of the other required packages) instead of relying on conda to manage everything.

MikeAxtell commented 9 months ago

Closing due to inactivity.