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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)

Image RemovedImage Added

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:


HomeWorkWork2Scratch
quota10 GB1024 GB = 1 TB2+ PB (basically infinite)
policybacked upnot backed up,
not purged
not backed up,
purged if not accessed recently (~10 days)
access commandcdcdwcdw2cds
environment variable$HOME$STOCKYARD (root of the shared Work file system)
$WORK $WORK2 (different sub-directory for each cluster)
$SCRATCH
root file system/home/workwork2/scratch
use forSmall 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).

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Code Block
--------------------- 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.

Code Block
languagebash
titleChanging file systems at TACC
cdwcdw2
cds
cd
Tip

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.

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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 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

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Code Block
languagebash
titleThe shared BioITeam directory
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.

Code Block
languagebash
titleOur shared class directory
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.

Code Block
languagebash
titleThe legacy BioITeam directory on Corral
ls /corral-repl/utexas/BioITeam

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!

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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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Code Block
languagebash
titleGet ready to wget
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:

Code Block
languagebash
titlewget to retrieve a web URL
wget http://web.corral.tacc.utexas.edu/BioITeamBioinformaticsResource/CoreNGS/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz

Now press Enter to get the command going. Repeat for the 2nd link. Check that you now see the two files (ls).

Tip

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

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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.

Code Block
languagebash
titleSingle file copy with cp
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".

Code Block
languagebash
titleDirectory copy with cp
mkdir -p $SCRATCH/data
cds
cd data
cp -r $CORENGS/general/ general/

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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
    • -rrecursively 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).

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Code Block
languagebash
titlersync (local directory)
mkdir -p $SCRATCH/data
cds
rsync -avWPavW $CORENGS/custom_tracks/ data/custom_tracks/

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Code Block
languagebash
rsync -avWPavW /work/projects/BioITeam/projects/courses/Core_NGS_Tools/custom_tracks/ data/custom_tracks/
Tip

The bash shell has several convenient line editing features:

  • use the Up arrow to scroll back through the command line history; Down arrow goes forward
  • use Ctrl-a to move the cursor to the beginning of a line; Ctrl-e to the end
  • use Backspace to remove text before the cursor; Delete to remove text after the cursor
  • use Ctrl-a and then Ctrl-k to delete all text on your command line

Copy from a remote computer - scp or rsync

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Code Block
titlesingle remote file copy with scp
mkdir -p $SCRATCH/data/test1
cds
cat $CORENGS/tacc/dragonfly_access.txt
cds
mkdir -p data/test2
scp corengstools@dragonfly.icmb.utexas.edu:~/custom_tracks/progeria_ctcf.vcf.gz ./data/test1test2/
ls ./data/test1test2

Notes:

  • 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

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Code Block
languagebash
titlersync (remote directory)
rsync -avWPavW corengstools@dragonfly.icmb.utexas.edu:~/custom_tracks/ ~/scratch/data/custom_tracks/

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Code Block
titlePlay a scavenger hunt for more practice
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?

Expand
titleAnswer

ls5stamp2:~/what/starts/here/changes/the/world

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Expand
titleStep 1 answer

From inside your ~/what directory:

Code Block
titlePlay a scavenger hunt for more practice
mkdir starts
cd starts
cp /workwork2/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/steps/nextInstr .
cat nextInst
Expand
titleStep 2 answer

From inside your ~/what/starts directory:

Code Block
titlePlay a scavenger hunt for more practice
mkdir here
cd here
wget http://web.corral.tacc.utexas.edu/BioITeamBioinformaticsResource/CoreNGS/step3.txt
cat step3.txt
Expand
titleStep 3 answer

From inside your ~/what/starts/here directory:

Code Block
titlePlay a scavenger hunt for more practice
scp -r /workwork2/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes/ changes/
# or
rsync -ptrvP /workwork2/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes/ changes/
# Note: rsync -avP ... will also work, but will report an error because the destination file and
# directory ownership cannot be changed to match the source. But the files will be copied, and
# ownership assigned to you.
 
# Then
cd changes 
more largeFile.txt

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