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Saskia-Oosterbroek / decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
MIT License
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Missing bcftools #32

Closed Fika182 closed 2 years ago

Fika182 commented 2 years ago

Hi @Saskia-Oosterbroek!

Thank you for such a great pipeline. It helps me a lot. But when I tried to run example data set, it showed message that I miss to install bcftools. Should I install it separately? Or maybe there's a way that may help me to install it?

Thank you!

Regards, Fika

Saskia-Oosterbroek commented 2 years ago

Hi Fika, It should be included in the decona environment through the installer. To check whether it has actually been installed you could check the bin in~/miniconda3/envs/decona/bin. If bcftools is there you might have overlooked activating the environment before running decona. You can use conda activate decona after which decona should work. If neither of these things are the issue then an error might have sneaked in at the last adjustments of the installer script! Please do let me know :)

You can add bcftools manually as well if everything else fails, you can install samtools in the decona environment.

Best, Saskia

Fika182 commented 2 years ago

I have checked the bin of decona and there's bcftools, but I don't know why it keeps informing me that bcftools hasn't been installed even I have activated decona through source activate decona. Does the conda version give an effect to this problem? I use Conda v. 4.3.31 recently.

Regards, Fika

Fika182 commented 2 years ago

Hi! I've installed bcftools in decona envs. Thanks for your great suggestion!