diff --git a/README.md b/README.md index b126c30943911a2da463013be322bb9b46f73ac7..f554643f5a48dc681b534fd505590528ec37efbb 100644 --- a/README.md +++ b/README.md @@ -16,28 +16,38 @@ OS_TYPE=x86_64 mkdir conda_installation cd conda_installation -RUN curl -LO "http://repo.continuum.io/miniconda/Miniconda3-${CONDA_VER}-Linux-${OS_TYPE}.sh" curl -LO "http://repo.continuum.io/miniconda/Miniconda3-${CONDA_VER}-Linux-${OS_TYPE}.sh" sudo bash Miniconda3-latest-Linux-x86_64.sh -p /miniconda -b sudo groupadd anaconda_admin sudo chown -R :anaconda_admin /miniconda sudo chmod -R 775 /miniconda sudo adduser nibio anaconda_admin -conda update conda -conda init +/miniconda/bin/conda update conda +/miniconda/bin/conda init + +``` +You should reboot shell session at this point. +``` + conda create --name pdal-env python=3.8.13 conda activate pdal-env conda install -c conda-forge pdal python-pdal + ``` You should reboot shell session at this point. Next, you should clone the repo with the following command: ``` -git clone git@github.com:maciekwielgosz/FSCT.git +git clone git@gitlab.nibio.no:maciekwielgosz/instance_segmentation_classic.git ``` if you didn't exchange ssh keys you may need to use the following command: - `git clone https://github.com/maciekwielgosz/FSCT.git` + `git clone https://gitlab.nibio.no/maciekwielgosz/instance_segmentation_classic` + +You have to install requirements for the repo. + ``` + pip install -r requirements.txt + ``` # Running the pipeline with the NIBIO code