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maxplanck-ie / HiCAssembler

Software to assemble contigs/scaffolds into chromosomes using Hi-C data
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HiCexplorer version #12

Open xinwang-bio opened 5 years ago

xinwang-bio commented 5 years ago

Hi Authors Which HiCexplorer version you used ? I have installed the latest version, But it shows No module named HiCMatrix. Thanks.

azkalot1 commented 5 years ago

Installing HiCexplorer 2.1.3 worked for me, not 3.0

vivekbhr commented 5 years ago

We removed HiCMarix module from hicExplorer in version 2.2 and made it a separate library. That might be the issue here. You can separately install HiCMatrix, or downgrade HiCEx version below 2.2

xinwang-bio commented 5 years ago

We removed HiCMarix module from hicExplorer in version 2.2 and made it a separate library. That might be the issue here. You can separately install HiCMatrix, or downgrade HiCEx version below 2.2

Thanks a lot. I will try the version below 2.2.

xinwang-bio commented 5 years ago

Installing HiCexplorer 2.1.3 worked for me, not 3.0

Thanks a lot. I will try version 2.1.3.

EarlyEvol commented 4 years ago

fyi Got the standalone HiCMatrix install to play nice with HICAssembler to be able to use HiCExplorer 3. All from a fresh miniconda3 install with pip

git clone https://github.com/deeptools/HiCMatrix.git
pip install ./HiCMatrix/

because this is all in miniconda, could just change HiCassembler.py and Scaffold.py to load HICMatrix from hicmatrix instead of hicexplorer with:

import hicexplorer.HiCMatrix as HiCMatrix

to

import hicmatrix.HiCMatrix as HiCMatrix

Seems to be working well.