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This page describes steps for former users of fourierseq.icmb.utexas.edu to migrate to using the BRCF GSAF POD.

Step 1 - Sign up for an BRCF account

See this discussion: Obtaining a BRCF Account.

Once you can login to the BRCF Account Management web page (https://rctf-account-request.icmb.utexas.edu) with your BRCF credentials and see that you have been granted access to the GSAF POD, proceed to Step 2.

Step 2 - Login to one of the GSAF POD compute servers

Use ssh to login to one of the GSAF POD compute servers. Note that your fourierseq home directory is now only available when you login to gsafcbig01.

• gsafcomp01.ccbb.utexas.edu
• gsafcomp02.ccbb.utexas.edu
• gsafcbig01.ccbb.utexas.edu
• gsafcbig02.ccbb.utexas.edu
  

See this table for more information on the GSAF POD: Available PODs

Step 3 - Locate your fourierseq home directory data

All fourierseq home directory data has been copied to an external storage area which is mounted on gsafcbig01 as /mnt/fourierseq, which is a read-only file system. Your home directory can be found under /mnt/fourierseq/userdata.

Step 4 - Migrate your fourierseq home directory data

Once you have located your fourierseq home directory, you should decide what to do with it. The contents of your transferred fourierseq home directory are read-only to you, so you may want to move some or all of it to where it can be both read and written.

Options are:

1. Copy it to your GSAF POD Home directory, which has a 100 GB user quota.
2. Copy it to a directory in your shared GSAF POD Work area, which has a 2 TB group quota.
3. Copy it to a directory in your shared GSAF POD Scratch area, which has a 5 TB group quota but is not backed up.
4. Leave it in the /stor/scratch/migration/fourierseq area and have it remain read-only and not be backed up.
5. ContactUs and request that it be deleted, or to request that it be assigned to your BRCF user account so you can delete it.

Please see this discussion for further information on Home, Work and Scratch areas on BRCF PODs: POD file systems.

For example, if you are in the Georgiou group, with BRCF user name brcfuser and fourierseq user name fsequser, wishing to migrate your data to your shared Work area, you could copy it as shown below (remember, this must be done from gsafcbig01 which is the only compute server where /mnt/fourierseq is mounted):

rsync -avrW /mnt/fourierseq/userdata/fsequser/ /stor/work/Georgiou/brcfuser/

Step 5 - Locate Scott and Dhivya's custom fourierseq scripts

There is a large amount of software installed on all BRCF POD compute servers. See this discussion for more information: POD Software Information

In addition, we have attempted to migrate custom scripts written by Scott Hunicke-Smith and Dhivya Arasappan to the GSAF POD. They can be found at:

• /stor/work/opt/scott_bin - Scott Hunicke-Smith scripts
• /stor/work/opt/daras_bin - Dhivya Arasappan scripts

We have not been able to exhaustively test these migrated scripts, so please ContactUs if you run into difficulties executing them.

Step 6 - Can I access my GSAF run data from the POD?

You may have used fourierseq 's FUSE mount of the GSAF iRODs data area (fourierseq:/raid/jcruz/corral) to access your GSAF sequencing data. We have implemented something similar on the GSAF POD, accessible only from the gsafcbig01 compute server.

Most of the GSAF sequencing data can be accessed on gsafcbig01 at the path gsafcbig01.ccbb.utexas.edu:/mnt/corral.

data is no longer available on the GSAF pod.