Installation

Linux

This installation instruction has been tested on Ubuntu Linux 18.04 and 19.04.

Suppose your Linux user directory is /home/foo. We will create two folders /home/foo/miniconda3 and /home/foo/software.

Please use the commands below to install scCloud locally via Miniconda:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh .
export CONDA_PATH=/home/foo
bash Miniconda3-latest-Linux-x86_64.sh -p $CONDA_PATH/miniconda3
mv Miniconda3-latest-Linux-x86_64.sh $CONDA_PATH/miniconda3
source ~/.bashrc
conda create -n scCloud -y pip
conda activate scCloud
mkdir -p $CONDA_PATH/software
git clone https://github.com/klarman-cell-observatory/scCloudPy.git $CONDA_PATH/software/scCloudPy
cd $CONDA_PATH/software/scCloudPy/scCloud
pip install -e .
cd $OLDPWD

Mac OS

Suppose your MacOS user directory is /Users/foo. We will create two folders /Users/foo/miniconda3 and /Users/foo/software.

Please use the commands below to install scCloud locally via Miniconda:

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
export CONDA_PATH=/Users/foo
bash Miniconda3-latest-MacOSX-x86_64.sh -p $CONDA_PATH/miniconda3
mv Miniconda3-latest-MacOSX-x86_64.sh $CONDA_PATH/miniconda3
conda create -n scCloud -y pip
mkdir -p $CONDA_PATH/miniconda3/envs/scCloud/etc/conda/activate.d
mkdir -p $CONDA_PATH/miniconda3/envs/scCloud/etc/conda/deactivate.d
printf '#!/bin/sh\n\nexport KMP_DUPLICATE_LIB_OK=true\n' > $CONDA_PATH/miniconda3/envs/scCloud/etc/conda/activate.d/env_vars.sh
printf '#!/bin/sh\n\nunset KMP_DUPLICATE_LIB_OK' > $CONDA_PATH/miniconda3/envs/scCloud/etc/conda/deactivate.d/env_vars.sh
conda activate scCloud
mkdir -p $CONDA_PATH/software
export MACOSX_DEPLOYMENT_TARGET=10.9
git clone https://github.com/klarman-cell-observatory/scCloudPy.git $CONDA_PATH/software/scCloudPy
cd $CONDA_PATH/software/scCloudPy/scCloud
pip install -e .
cd $OLDPWD
cd $OLDPWD

Use scCloud in UGER

First, you need to request a RedHat7 server:

qrsh -q interactive -l h_vmem=4g -l os=RedHat7 -P regevlab

Then, if you have installed scCloud, you could activate the virtual environment:

source activate scCloud

Or, you can use an installed version by typing:

source /ahg/regevdata/users/libo/miniconda3/bin/activate scCloud