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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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Installing HiCExplorer problem #519

Closed sshen82 closed 4 years ago

sshen82 commented 4 years ago

Hi, I am trying to install HiCExplorer 3.4.3 using conda, but failed. It installed 2.2 when I use "conda list" to see the packages.

hicexplorer 2.2 py36_0 bioconda

Also, it didn't install hic2cool, fit_nbinom automatically.

The procedure I did was first use "conda create -n myenv python=3.6", then after activating this virtual environment, I use "conda install hicexplorer -c bioconda -c conda-forge". Is there anything wrong with that?

sshen82 commented 4 years ago

When I use github, it just doesn't install other packages.

joachimwolff commented 4 years ago

conda create --name hicexplorer3.4.3 hicexplorer=3.4.3 -c bioconda -c conda-forge and conda activate hicexplorer3.4.3

For some reasons I do not understand the default is still set to version 2.2 and you need to specify the version number.

sshen82 commented 4 years ago

Ok, this question is solved, but when I type "hicConvertFormat -m matrix.hic --inputFormat hic --outputFormat homer -o matrix.homer" in shell, it doesn't show any error, but also doesn't show the output.

joachimwolff commented 4 years ago

As written in our documentation, the conversion from hic is only possible to cool. However, from cool you can convert to homer.

https://hicexplorer.readthedocs.io/en/latest/content/tools/hicConvertFormat.html#hicconvertformat