Installation Using Conda

Date:

2023-12-12

0. Clean up

Clear Conda Temporary Files

conda clean -a

Clear Pip Temporary Files

pip cache purge

1. Create Conda Environment

conda create -y -n giotto_suite python=3.10 r=4.2
conda activate giotto_suite

export PKG_CONFIG_PATH=$CONDA_PREFIX/envs/giotto_suite/lib/pkgconfig
# export PKG_CONFIG_PATH=/sc/arion/work/wangw32/conda-env/envs/giotto_suite_bento_install/lib/pkgconfig

2. Install Giotto

2.1 Install Dependency Packages

Install these packages first, as they may encounter network issues during Giotto’s installation. Use conda for installation.

conda install -y -c conda-forge -c bioconda -c r -c defaults r-gert
conda install -y -c conda-forge -c bioconda -c r -c defaults r-magick r-terra r-igraph
# For other dependencies with installation issues, use conda:
# conda install -y -c conda-forge -c bioconda -c r -c defaults r-sf

2.2 Check R_LIB

library_paths <- .libPaths()
print(library_paths)
# [1] "/sc/arion/work/wangw32/conda-env/envs/giotto_suite/lib/R/library"

2.3 Install Devtools & Giotto

options(timeout=1000)

# Necessary for installation from R
if(!"devtools" %in% installed.packages()) {
  install.packages("devtools")
}

devtools::install_github("drieslab/Giotto")

3. Install Python Dependency Packages

Install Necessary Python Packages.

conda activate giotto_suite
conda install -y cmake
pip install pandas python-igraph networkx python-louvain leidenalg scikit-learn smfishHmrf

Install Other Packages (Optional).