Setting up the environment for bioflows

This section is specifically aimed at users of Brown University's OSCAR HPC cluster. Users of other systems should pay close attention to the file paths used, as they may be different for their particular system.

Setup conda environment

Setup on OSCAR HPC Cluster at Brown University

First load the cbc_conda environment as follows:

source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda

Note

Sometimes it may appear that there is no response. In that case make sure to wait for 2-3 minutes and the use cntrl-c to interrupt. You should see something like the below in your command prompt

   (cbc_conda_v1) [your_ccv_username@login004 mydir]

run the echo $PATH command to confirm that /gpfs/runtime/cbc_conda/cbc_conda_v1_root/envs/cbc_conda_v1/bin is the first element in the list of paths in your output.

Error in Paths

If /gpfs/runtime/cbc_conda/cbc_conda_v1_root/envs/cbc_conda_v1/bin is not the first element in the list, then use the command

   export PATH=/gpfs/runtime/cbc_conda/cbc_conda_v1_root/envs/cbc_conda_v1/bin:$PATH

This will add /gpfs/runtime/cbc_conda/cbc_conda_v1_root/envs/cbc_conda_v1/bin to the beginning of your PATH variable

For convenience we will use /users/username as the working directory. You should modify this parameter to reflect the path to your own preferred working directory.

Setup on other systems

Install conda from anaconda following their installation instruction

Setup GNU screen session

These scripts should be run in a persistent terminal session and we will use GNU screen to do that, which will allow us to disconnnect from our ssh sessions without disrupting long running jobs. To learn more on how to use screen use the following link gnu screen tutorial

Change into your working directiory and start a screen session naming it test_bioflows as shown below:

cd /users/username
screen -S test_bioflows

Once you are in your screen session, set up your conda environment containing bioflows

source /gpfs/runtime/cbc_conda/activate_cbc_conda

Activating the conda environment may take a few moments, but you should see a prompt that looks like

(cbc_conda_v1) [your_ccv_username@login004 ~]$

If you don't see the prompt, you may need to press enter again (or cntrl-c)to get your terminal window to refresh. Now you are ready to run the predefined workflows in the tutorials.