SMRTLINK on Condo

Before you begin

Email hpc-help@iastate.edu requesting access to SMRTLink on Condo.

Accessing SMRTLink

Go to smrtlink.its.iastate.edu (Note: Only works on Google Chrome web browser)

Login with your ISU Net-ID and password.

Managing Data

SMRTLink User Guide attached below provides a general overview on navigating and using SMRTLink. There are, of course, a few things that the users need to be aware of to use it on Condo.

The SMRTLink input directory is located at

All users need to copy their input data to this directory as SMRTLink has read privileges for this directory alone (the data will still be owned by the respective user). It is suggested that the project investigator (Bioinfomatician in SMRTLink) create a directory in /work/smrtanalysis that can be easily identified by project members and copy relevant data there. SMRTLink will not write any data to this directory, all the intermediate and final output will be stored in $SMRT_ROOT/userdata within the respective job ID. ($SMRT_ROOT on CONDO is at /shared/hpc/smrtanalysis/smrtlink/userdata/jobs_root )

Once done with staging the data, the user can login to SMRTLink portal and import the data

Data Management -> Import -> SMRT Link server -> Select data type -> Navigate to /work/smrtanalysis/{directory} -> import

After successful import, you will see your data under "Data Sets"

Starting Analyses

Click on the data set and on the next screen select "Analyze.."

Select the required Analysis application and click "Start"

Output Management

After successful analysis, the "Analysis Result" page will have all the output data from your run.

The output data will be deleted in 90 days as per the policy of Large short-term storage on Condo (since all the intermediate and output data are saved in ptmp). It is important that you download all the output data as soon as possible - once deleted the data cannot be recovered.

For any assistance or trouble shooting, please email hpc-help@iastate.edu

SMRTLink User Guide