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qinqian / lisa

epigenome analysis to rank transcription factors
http://lisa.cistrome.org
MIT License
29 stars 4 forks source link

could you please provide a environment.yml file that allow lisa installation? #6

Closed jchenpku closed 3 years ago

jchenpku commented 3 years ago

I used the environment.yml from the repository and also tried to install different version of pandas /numpy but always ended up with confliction. Thanks.

qinqian commented 3 years ago

Hi,

The environment.yml is obsoleted. Please follow the latest readme to install the Lisa command line:

wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
export PATH="${HOME}/miniconda3/bin:$PATH"

conda config --add channels defaults && conda config --add channels conda-forge && conda config --add channels bioconda && conda install mamba -c conda-forge && mamba create -n lisa -c qinqian lisa_minimal python=3.6.6

#or 

conda config --add channels defaults && conda config --add channels conda-forge && conda config --add channels bioconda && conda install mamba -c conda-forge && mamba create -n lisa -c qinqian lisa=1.0 python=3.6.6

export MKL_THREADING_LAYER=GNU

In addition, we have a more efficient version recently released, which is worth exploring as well.

Best, Qian