Where to get Juicebox command line tools

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Aoi Summer

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Apr 19, 2017, 2:24:47 AM4/19/17
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Hi, 

I want to generate .hic files from HiC-Pro results where juicebox is needed.
The two version of command line tools ("juicebox_tools.jar" and "Juicebox_CLT.jar") can't be found in juicebox or juicer folders. 
Juicebox.jar

Is there anyone know how to download this tool?

Thanks so much.
Aoi

Muhammad Saad Shamim

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Apr 19, 2017, 2:51:32 AM4/19/17
to Aoi Summer, 3D Genomics

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Aoi Summer

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Apr 19, 2017, 3:08:33 AM4/19/17
to 3D Genomics, stca...@gmail.com
Thanks a lot, the tool I want is juicebox_tools.jar. I found it via your link.
Regards,
Aoi


On Wednesday, April 19, 2017 at 2:51:32 PM UTC+8, Muhammad Shamim wrote:
Sure, the jar can be downloaded from here:
On Wed, Apr 19, 2017 at 1:24 AM, Aoi Summer <stca...@gmail.com> wrote:
Hi, 

I want to generate .hic files from HiC-Pro results where juicebox is needed.
The two version of command line tools ("juicebox_tools.jar" and "Juicebox_CLT.jar") can't be found in juicebox or juicer folders. 
Juicebox.jar

Is there anyone know how to download this tool?

Thanks so much.
Aoi

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Neva Durand

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Apr 19, 2017, 3:10:23 AM4/19/17
to Aoi Summer, 3D Genomics
Hello,

Just a note, we've renamed things due to some confusion about functions.  To create hic files, you use juicer_tools.jar.  There is no longer a juicebox_tools.jar.

Best
Neva

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Neva Cherniavsky Durand, Ph.D.
Staff Scientist, Aiden Lab

Aoi Summer

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Apr 19, 2017, 3:13:05 AM4/19/17
to 3D Genomics, stca...@gmail.com

wget http://hicfiles.s3.amazonaws.com/internal/juicebox_tools/8.5.16/juicebox_tools.jar

I download juicebox_tools.jar by wget, is this the same thing as juicer_tool.jar?

Neva Durand

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Apr 19, 2017, 4:02:38 AM4/19/17
to Aoi Summer, 3D Genomics
This is an old jar (August 2016).

The link Muhammad sent has the latest:  https://github.com/theaidenlab/juicer/wiki/Download

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