--cpu option unavailable on docker

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Alissa Cullen

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Apr 17, 2025, 1:52:33 AMApr 17
to 3D Genomics
I am attempting to run this .hic file -> https://www.ncbi.nlm.nih.gov/sra/SRX5247015[accn] through HICCUPS via CPU (https://github.com/aidenlab/juicer/wiki/CPU-HiCCUPS), however when in the docker from the Aiden lab, there is no option for --cpu

"juicer_tools hiccups --help" output:
"Usage:   juicer_tools hiccups [-m matrixSize] [-k normalization (NONE/VC/VC_SQRT/KR)] [-c chromosome(s)] [-r resolution(s)] [-f fdr] [-p peak width] [-i window] [-t thresholds] [-d centroid distances] [--ignore_sparsity]<hicFile> <outputDirectory> [specified_loop_list]"

 and when I try to run my file through with 
"juicer_tools hiccups --cpu --threads 4 --ignore_sparsity xx.hic /output/path"
I am receving this error: 
"Exception in thread "main" jargs.gnu.CmdLineParser$UnknownOptionException: Unknown option '--cpu'
        at jargs.gnu.CmdLineParser.parse(CmdLineParser.java:475)
        at jargs.gnu.CmdLineParser.parse(CmdLineParser.java:426)
        at juicebox.tools.HiCTools.main(HiCTools.java:63)"


Any help would be appreciated!
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