edit dockerfile for automatical bedtools/bcftools installation.

LiuzLab / AI_MARRVEL

AI-MARRVEL (AIM) is an AI system for rare genetic disorder diagnosis

GNU General Public License v3.0

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edit dockerfile for automatical bedtools/bcftools installation. #26

Closed hyunhwan-bcm closed 3 months ago

hyunhwan-bcm commented 3 months ago

related to #25

arine commented 3 months ago

Need to update Installation Doc

SpicyChicken6 commented 2 months ago

Do you mind checking on this edit again? I think the bedtools installed this way couldn't work in docker, probably need to move bedtools to a different folder within docker:

# Install bedtools
RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary \
    && mv bedtools.static.binary /usr/local/bin/bedtools

Thank you,

hyunhwan-bcm commented 2 months ago

bedtools used like this way:

https://github.com/LiuzLab/AI_MARRVEL/blob/0c6e6f15c5a14584e7e4527732c880bbf4b53696/run/simple_repeat_anno.py#L17

so basically it doesn't break anything. Thanks for checking

SpicyChicken6 commented 2 months ago

bedtools used like this way:

https://github.com/LiuzLab/AI_MARRVEL/blob/0c6e6f15c5a14584e7e4527732c880bbf4b53696/run/simple_repeat_anno.py#L17

so basically it doesn't break anything. Thanks for checking

Sorry I didn't check on the use of it. Thanks Hwan!