The instructions in this blog were written to set up the lab in Rstudio cloud

Setting up your own system

Linux is the operating system of choice to run bioinformatics software. You will need either a computer running linux or or mac os, which has a linux-like environment.

  • install anaconda/miniconda
  • define imlabtools conda environment how to here, which will install all the python modules needed for this analysis session
  • download data and software from Box. This will have copies of all the software repositories and the models
  • download software
    • download metaxcan repo
  • download prediction models from
  • install R/RStudio/tidyverse package
  • install R packages
  • git clone
  • start Rstudio (if you installed workflowr, you can just open the QGT-Columbia-HKI.Rproj)

R setup

#install R packages 
remotes::install_github("stephenslab/susieR") #gives the most up to date SusieR 
remotes::install_github("simingz/ctwas", ref = "develop")

#cTWAS install
remotes::install_github("simingz/ctwas", ref = "develop")

## make sure these are installed
# library(data.table)
# library(BEDMatrix)
# library(Rfast)
# library(susieR)
# library(coloc)

#installing base miniconda

Setting up Conda Environment

#adding path
export PATH=$PATH:/cloud/project/miniconda/bin
# adding repos/data
git clone
git clone
conda config --append channels conda-forge
conda config --append channels bioconda
conda env create -f /cloud/project/MetaXcan/software/conda_env.yaml
conda activate imlabtools

Set the Ram to 5gb in order to create the environment.

Box Data

To upload the data. I first downloaded the box folder onto a local machine and then compressed the folders in the box folder to upload onto the server.

Notes: For some reason setting up the environment and uploading the data will continue to use a lot of background RAM set sure to close the project and reopen to close extraneous programs.


Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The source code is licensed under MIT.

Suggest changes

If you find any mistakes (including typos) or want to suggest changes, please feel free to edit the source file of this page on Github and create a pull request.