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vatlab / varianttools

software tool for the manipulation, annotation, selection, and analysis of variants in the context of next-gen sequencing analysis
https://vatlab.github.io/vat-docs/
GNU General Public License v3.0
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SPECFILE not available in Variant Simulation Tools #153

Closed enigmargs closed 3 years ago

enigmargs commented 3 years ago

Hi,

I'm trying to use the existing simulation models and I've installed VST using conda (v 3.1.3) and my python version is 3.8.10. When I run, vtools show simulation SPECFILE it throws error ERROR: Unrecognized simulation model neutral: Failed to download pipeline specification file neutral.pipeline: Failed to download simulation/neutral.pipeline because it is not in the variant tools online repository or local stash directories.

The command vtools simulate Peng2014_ex1 neutral throws, _ERROR: Failed to simulate replicate 0 of model Peng2014_ex1: Failed to execute step neutral1: Failed to import module simuPOP.demography: No module named 'simuPOP'

Am I supposed to install any module before running this simulation? I can't see any information on this.

Any help is greatly appreciated.

BoPeng commented 3 years ago

I apologize but VST has deprecated and no longer under maintenance.

enigmargs commented 3 years ago

Thank you @BoPeng for the quick response. Sad to hear that. I came here from GSR site as I want to simulate WES data for my work. Would really appreciate if you can recommend any similar software to simulate WES data like VST.

Many thanks,

BoPeng commented 3 years ago

There are a number of simulators. What particular features are you looking for?