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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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hicpro2juicebox.sh: line 152: java: command not found #617

Closed qqyanyang closed 8 months ago

qqyanyang commented 8 months ago

Hi, I have a issue about the hicpro2juicebox.sh. When I use the commond ''bash hicpro2juicebox.sh -i /mypath/GSM.allValidPairs -j /juicertools_path/juicer_tools.1.9.9_jcuda.0.8.jar -g hg19 -o /myoutpath, there is a issue that:
HiC-Pro format > 2.7.5 detected ... Generating Juicebox input files ... Running Juicebox ... hicpro2juicebox.sh: line 152: java: command not found done !

How could I solve this issue?Thanks~

nservant commented 8 months ago

Just add your JAVA in your PATH