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PouletAxel / SIP

SIP: Significant Interaction Peak caller
GNU General Public License v3.0
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coolTools path #11

Closed gdolsten closed 3 years ago

gdolsten commented 3 years ago

Hi, when we are using SIP, how are we supposed to provide the path to cooler? Is it just the directory containing cooler? Right now I am running:

java -jar ~/SIP/SIP_HiC.jar cool data.mcool chrom.sizes sip_loops.txt ~/cools/cooltools ~/cools/cooler

But I get the following error: Cannot run program "/Genomics/grid/users/gdolsten/cools/cooltools": error=13, Permission denied

cools/cooltools looks like: balance.py cli contrast.py coverage.py directionality.py dotfinder.py eigdecomp.py expected.py init.py insulation.py io lib main.py pycache saddle.py sample.py snipping.py

PouletAxel commented 3 years ago

Hi, your cooler and cooltools are not directory but binary file, on my laptop for example: ~/anaconda3/bin/cooler

gdolsten commented 3 years ago

Thank you, my concerns are answered

PouletAxel commented 3 years ago

java -jar SIP_HiC.jar cool ~/Desktop/SIP/testCooler/4DNFIWO9BDFZ.mcool hg38.sizes ~/Desktop/Cool/ ~/anaconda3/bin/cooltools ~/anaconda3/bin/cooler -g 1.5 -mat 2000 -d 5 -res 5000 -t 2000 -cpu 3

you can choose you resolution with -res