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Teichlab / gene2probe

Pipeline for designing custom probes against human genes
MIT License
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installation steps in Readme.md does not work #1

Open timrandg opened 1 month ago

timrandg commented 1 month ago

I followed the installation steps, but the pybedtools will not import. The issue seems to be that python 3.11 and pydebtools are not compatible. I reverted to python 3.7, which allowed import pybedtools in ipython.

Jupyter may not recognize the python used in the conda env...that can be fixed with nb_conda_kernels.

conda install -n nb_conda_kernels

Be sure to select the kernel associated with your env.

I may be back with other issues.

timrandg commented 1 month ago

I added an install.sh script that may make the installation process better. Please see pull request.

ioansarr commented 1 month ago

Hi Tim! Thank you for using our tool and for reporting this issue.

In my conda installation, I am using python 3.11.9 and pybedtools 0.10.0 without any issues. Could you please forward the error you encountered during installation?

To use the jupyter notebooks interactively (as intended), it is indeed important to set up an ipykernel and select the correct kernel in the jupyter lab session. I will add instructions for this to the README file.