Tips on Biowulf for Partek Flow Users

Even though Partek Flow runs on Biowulf, the NIH Unix-based high performance computing cluster, users do not need to be experts in command line to use this software. However, there are somethings that are useful to know because Partek Flow projects, input, and output are all stored on Biowulf.

Signing onto Biowulf

To sign onto Biowulf, open a Terminal if using MacOS or Command Prompt if using Windows 10 or above. Once opened, at the prompt, do the following to sign on. The breakdown of the command is as follows.

• ssh: Connect to remote computer (ie. Biowulf)
• user: User's NIH username
• @biowulf.nih.gov: The remote computer to connect to (ie. NIH Biowulf)

ssh user@biowulf.nih.gov

Users will then be asked to enter a password for signing onto Biowulf. This is the password that the user utilizes to sign onto NIH applications. The password will not appear as the user is typing but keep typing and hit enter when done.

user@biowulf.nih.gov's password:

Changing into the User's Data Folder

Upon signing onto Biowulf, users will land in the /home/user directory (again replace user with user's NIH username). This directory only has 16 GB of storage space and cannot be increased, thus users will need to perform analyses in the /data/user folder. Further, a folder called /PartekFlow in the /data/user directory is created when the Partek Flow account is activated for the user.

To check which folder on Biowulf a user is currently in, use the pwd command.

Upon signing onto Biowulf:

pwd

/home/user

To change into the user's data folder do the following.

cd /data/user

Biowulf staff will create a folder called PartekFlow in the user's /data/user directory upon activating a Partek Flow account. This folder contains all Partek Flow projects, inputs, outputs, and data Uploads.

List the contents of the /data/user folder.

ls /data/user

PartekFlow

Change into the PartekFlow folder.

cd /data/user/PartekFlow

The PartekFlow folder houses project folders (only if users have projects), which contain input and output as well a folder called uploads that stores data that has been loaded to the NIH Partek Flow server.

Project_RNAsequencing_1234
uploads