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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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How to find halLiftover from cactus install? #1411

Closed hopehealey closed 5 months ago

hopehealey commented 5 months ago

Hi Cactus team,

I would like to use the halLiftover tool from the Hal package to transfer phastcons conserved element annotations from one species to another. From the Hal GitHub, it seems as though I should not need to install Hal if I already have cactus in my system. Since I have cactus installed and working properly, I was wondering how to find the halLiftover command within cactus. If I try to run cactus-halLiftover, it does not find the command. I noticed that the hal2chains uses halLiftover, so I know it should be there somewhere. Does anyone have tips to find halLiftover?

Thank you, Hope

glennhickey commented 5 months ago

Yeah, hal's included in the cactus releases in cactus/bin. If you've installed cactus correctly, you should be able to run halLiftOver or any other hal tool after activating the cactus environment.