|TACC storage areas and Linux commands to access data |
(all commands to be executed at TACC except
laptop-to-TACC copies, which must be executed on your laptop)
Local file systems
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:
|quota||10 GB||1024 GB = 1 TB||2+ PB (basically infinite)|
|policy||backed up||not backed up,|
|not backed up,|
purged if not accessed recently (~10 days)
|environment variable||$HOME||$STOCKYARD (root of the shared Work file system)|
$WORK $WORK2 (different sub-directory for each cluster)
|root file system||/home||/workwork2||/scratch|
|use for||Small files such as scripts that you don't want to lose.||Medium-sized artifacts you don't want to copy over all the time. For example, custom programs you install (these can get large), or annotation file used for analysis.||Large files accessed from batch jobs. Your starting files will be copied here from somewhere else, and your final results files will be copied elsewhere (e.g. stockyard, corral, or your BRCF POD).|
--------------------- 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 | -------------------------------------------------------------------------------
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
The cd (change directory) command with no arguments takes you to your home directory on any Linux/Unix system. The cdw cdw2 and cds commands are specific to the TACC environment.
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.
- $STOCKYARD - This refers to the root of your shared Work area
- e.g. /work/01063/abattenh (should be changed to /work2/01063/abattenh soon)
- e.g. /work/01063/abattenh (should be changed to /work2/01063/abattenh soon)
- $WORK or $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
- /workwork2/01063/abattenh/stampede2 on stampede2
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
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.
A couple of things to keep A couple of things to keep in mind regarding corral:
- corral is a great place to store data in between analyses.
- Store your permanent, original sequence data on corral
- Copy the data you want to work with from corral to $SCRATCH
- Run your analyses (batch jobs)
- Copy your results back to corral
- Occasionally corral can become unavailable. This can cause any command to hang that tries to access corral data!
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).
- 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.
mkdir -p $WORK$SCRATCH/archive/original/20202021.core_ngs cd $WORK$SCRATCH/archive/original/20202021.core_ngs wget
Here are two web links:
Right-click (Windows) or Control+click (Mac) on the 1st link in your browser, then select "Copy link location" from the menu. Now go back to your Terminal. Put your cursor after the space following the wget command then either right-click (Windows), or Paste (Command-V on Mac, Control-V on Windows). The command line to be executed should now look like this:
Now press Enter to get the command going. Repeat for the 2nd link. Check that you now see the two files (ls).
By default wget creates a file in the current directory matching the last component of the URL (e.g. Sample_Yeast_L005_R1.cat.fastq.gz here). You can change the copied file name with wget's -O option.
Also note that if you execute the same wget more than once, subsequent local files will be named with a .1, .2, etc. suffix.
Copy from a corral location - cp or rsync
cp [options] <source file 1> <source file 2> ... <destination directory>/
Make a directory in your scratch Scratcharea and copy a single file to it. The trailing slash ( / ) on the destination says it the destination is a directory.
mkdir -p $SCRATCH/data/test1 cp $CORENGS/misc/small.fq $SCRATCH/data/test1/ ls $SCRATCH/data/test1 # or.. mkdir -p ~/scratch/data/test1 cd ~/scratch/data/test1 cp $CORENGS/misc/small.fq . ls
Copy an entire directory to your scratch Scratch area. The -r argument option says "recursive".
mkdir -p $SCRATCH/data cds cd data cp -r $CORENGS/general/ general/
Both the source and target directories are local (in some file system accessible directly from ls5 stampede2). Either full or relative path syntax can be used for both. The -avP avW options above stand for:
- -a means "archive mode", which implies the following options (and a few others)
- -p – preserve file permissions
- -t – preserve file times
- -l – copy symbolic links as links
- -r – recursively copy sub-directories
- -v means verbose
- -W means transfer Whole file only
- Normally the rsync algorithm compares the contents of files that need to be copied and only transfers the different parts.
- For large files and binary files, figuring out what has changed (diff-ing) can take more time than just copying the whole file.
- The -W option disables file content comparisons (skips diff-ing).
mkdir -p $SCRATCH/data cds rsync -avWPavW $CORENGS/custom_tracks/ data/custom_tracks/
rsync -avWPavW /work/projects/BioITeam/projects/courses/Core_NGS_Tools/custom_tracks/ data/custom_tracks/
The bash shell has several convenient line editing features:
Copy from a remote computer - scp or rsync
mkdir -p $SCRATCH/data/test1 cds cat $CORENGS/tacc/dragonfly_access.txt cds mkdir -p data/test2 scp firstname.lastname@example.org:~/custom_tracks/progeria_ctcf.vcf.gz ./data/test1test2/ ls ./data/test1test2
- The 1st time you access a new host the SSH security prompt will appear
- You will be prompted for your remote host password
- The -r recursive argument works for scp also, just like for cp
rsync -avWPavW email@example.com:~/custom_tracks/ ~/scratch/data/custom_tracks/
cd cp -r /workwork2/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/what what # or using the $CORENGS environment variable cp -r $CORENGS/linuxpractice/what what cd what cat readme
Where are you when you're all done?
From inside your ~/what directory:
From inside your ~/what/starts directory:
From inside your ~/what/starts/here directory: