where to get juicebox CLT

[doug]

I would like to use the CLT but am not sure where to get them.  I have downloaded both the DMG and the jar files but I don't see any thing called "juicebox_tools.jar" as indicated in the online CLT documentation.  

I.e. "The juicebox script can be used in place of the unwieldy java -Xms512m -Xmx2048m -jar juicebox_tools.jar on Unix and Mac systems."

The README on github has a slightly different version of the text that reads

"The "juicebox" script can be used in place of the unwieldy "java -Xms512m -Xmx2048m -jar Juicebox_CLT.jar" on Unix and Mac systems."

I also searched the github repository for "juicebox_tools.jar" but didn't find any mention of it.  Searching for "Juicebox_CLT.jar" finds mentions of it but no file with that name.

I have also tried running juicebox-master/native_launcher/juicebox.sh but I get the error:

Error: Unable to access jarfile Juicebox_CLT.jar

So how do I download and run the CLT

Thanks so much.

[Machol, Ido]

Hi Doug,

Please take a look at: 

https://github.com/theaidenlab/juicer/tree/master/AWS/scripts

juicebox_tools.jar is located there.

juicebox_tools.jar and juicebox_CLT.jar are different names for the same thing.

If your script is using CLT, just rename that jar to the correct name.

Best,

Ido

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