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There are 3 local file systems available on any TACC compute cluster (Lonestar5stampede2, stampede2 lonestar5, etc.), each with different characteristics. All these local file systems are very fast and set up for parallel I/O (Lustre file system).

On ls5 stampede2 these local file systems have the following characteristics:

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--------------------- Project balances for user abattenh ----------------------
| Name           Avail SUs     Expires | Name           Avail SUs     Expires |
| genomeAnalysis       673  2021-03-31 | BioinformaticsResour 100  2020-06-30 |
| UT-2015-05-18       1000  2021-03-31 | DNAdenovo           4969  2021-03-31 |
| CancerGenetics      4856  2020-09-30 | A-cm10              8867  2020-12-31 |
------------------------ Disk quotas for user abattenh ------------------------
| Disk         Usage (GB)     Limit    %Used   File Usage       Limit   %Used |
| /home1              0.0      10.0     0.10          153     1000000    0.02 |
| /workwork2             614.5    1024.0    60.01        61094     3000000    2.04 |
| /scratch         2676.6       0.0     0.00        32442           0    0.00 |
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When you first login, you start in your home directory. Use these the cd, cdw2 and cds commands to change to your other file systems. Notice how your command prompt helpfully changes to show your location.

cdwcdw2
cds
cd

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TACC compute clusters now share a common Work file system called stockyard. So files in your Work area do not have to be copied, for example from ls5 to stampede2 to ls5 – they can be accessed directly from either cluster.

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• $STOCKYARD - This refers to the root of your shared Work area
  • e.g. /work/01063/abattenh  (should be changed to /work2/01063/abattenh soon)
    
• $WORK $WORK2 - Refers to a sub-directory of the shared Work area that is different for different clusters, e.g.:
  
  • /work/01063/abattenh/lonestar on ls5
  • /work/01063/abattenh/stampede2 on stampede2

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ls /workwork2/projects/BioITeam

Files we will use in this course are in a sub-directory there. The $CORENGS environment variable set in your login profile refers to this path.

echo $CORENGS
ls /workwork2/projects/BioITeam/projects/courses/Core_NGS_Tools

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corral is a gigantic (multiple PB) storage system (spinning disk) where researchers can store data. UT researchers may request up to 5 TB of corral storage through the normal TACC allocation request process. Additional space on corral can be rented for ~$85~$80/TB/year.

The UT/Austin BioInformatics Team also has an older, common directory area on corral.

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Once that data is staged to the ranch disk it can be copied to other places. However, the ranch file system is not mounted as a local file system from the stampede2 or ls5 clusters. So remote copy commands are always needed to copy data to and from ranch (e.g. scp, rsync).

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• original – for original sequencing data (compressed FASTQ files)
  • sub-directories named, for example, by year_month.<project_name>
• aligned – for alignment artifacts (BAM files, etc)
  • sub-directories named, e.g.,  by year_month.<project_name>
• analysis – further downstream analysis
  • reasonably named sub-directories, often by project
• genome refs – reference genomes and other annotation files used in alignment and analysis
  
  • sub-directories for different reference genomes
  • e.g. ucsc/hg19, ucsc/sacCer3, mirbase/v20
• code – for scripts and programs you and others in your organization write
  • ideally maintained in a version control system such as git, subversion or cvs.
  • easiest to name sub-directories for people.

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mkdir -p $WORK$WORK2/archive/original/20202021.core_ngs
cd $WORK$WORK2/archive/original/20202021.core_ngs
wget 

Here are two web links:

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