Setup GradVI workbench

Here is a short documentation to setup the environment for running GradVI experiments at the NYGC cluster.

Install R packages

devtools::install_github("stephenslab/mr.ash.alpha")
install.packages("genlasso")

Install Python packages

conda install patsy
cd ~/software
git clone git@github.com:stephenslab/gradvi.git
cd gradvi
pip install -e .
cd ~/software
git clone git@github.com:banskt/mr-ash-pen.git
cd mr-ash-pen
pip install .

I could not install the editable version of the package. I also could not install fpydemo using the -e flag. The normal installation was smooth, but the editable version failed while trying to link the same file multiple times. I ran out of time for debugging, but this needs to be solved later.

Install DSC

  • Prerequisites that can be installed with conda
conda install networkx sympy pyarrow sqlalchemy
conda install h5py sos sos-pbs
  • Install DSC
git clone git@github.com:stephenslab/dsc.git
cd dsc
pip install .

Output:

Successfully built dsc msgpack-python PTable
Installing collected packages: PTable, msgpack-python, numexpr, dsc
Successfully installed PTable-0.9.2 dsc-0.4.3.5 msgpack-python-0.5.6 numexpr-2.8.4
  • Check installation
dsc --version
dsc-query --version
  • Install R utilities for DSC
setwd("/gpfs/commons/home/sbanerjee/software/dsc/dscrutils")
getwd()
devtools::install_local('.')
system("dsc-query --version")