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jvollme/howto_install_groopm2.md

Last active September 5, 2022 19:24
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installing groopm2
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howto_install_groopm2.md

###a.) first create env with most dependencies:

conda create -n groomp2 python=2.7 matplotlib scipy bamm cython pillow pytables tempdir diamond hmmer pplacer mfqe orfm

###b.) obtain pip3 and use it to install singlem globally (while currently in the base environment OR any python3 environment)

sudo apt update
sudo apt install python3-pip
conda deactivate
conda deactivate # deactivate not only conda environment but also conda entirely (until you don't even see the base einvironment)
sudo pip3 install --no-cache-dir pandas==1.0.5 singlem # apparently tehre can be some pandas conflicts with sortm, so better to use the older version?

(singlem will automatically be in PATH for all environments, since it was installed globally)

###c.) switch to groopm2 conda environment, download groopm2 and install

conda activate #activate conda again
conda activate groopm2 
git clone https://github.com/timbalam/GroopM.git 
cd GroopM 
python setup.py install
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