Page History

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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 lonestar6, 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 lonestar6 these local file systems have the following characteristics:

	Home	Work	Scratch
quota	10 GB	1024 GB = 1 TB	2+ PB (basically infinite)
policy	backed up	not backed up, not purged	not backed up, purged if not accessed recently (~10 days)
access command	cd	cdw	cds
environment variable	$HOME	$WORK (different sub-directory for each cluster) $STOCKYARD (root of the shared Work file system ) $WORK (different sub-directory for each cluster )	$SCRATCH
root file system	/home	/work	/scratch
use for	Small files such as scripts that you don't want to lose.	Medium-sized artifacts files 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), or your organization's storage area.

When you first login, the system gives you information about disk quota quotas and your compute allocation quota:balance in "SU" (system units).

Code Block

--------------------- Project balances for user abattenh ----------------------
| Name           Avail SUs     Expires | Name           Avail SUs     Expires |
| genomeAnalysisOTH21095       673  2021-03-31 | BioinformaticsResour 1001000  20202022-0609-30 |
| UT-2015-05-18MCB21106       1000  2021-03-31 | DNAdenovo  995  2022-12-31 |
| OTH21164     4969  2021-03-31 |
| CancerGenetics      48561000  20202022-0912-3031 | A-cm10OTH21037            4224  8867  20202022-12-31 |
------------------------ Disk quotas for user abattenh ------------------------
| Disk         Usage (GB)     Limit    %Used   File Usage       Limit   %Used |
| /home1              0.0      1011.07     0.1000           52      153     10000000    0.0200 |
| /work             614169.50    1024.0    6016.0150        6109479362     3000000    2.04 |
| /scratch         2676.6       0.0     0.00        32442           0    0.00 |
-65 |
---------------------------------------------------------------------------------------------------

changing TACC file systems

When you first login, you start in your home Home directory. Use these the cd, cdw and cds commands to change to your other file systems. Notice how your command prompt helpfully changes to show your location.

...

Tip

The cd (change directory) command with no arguments takes you to your home directory on any Linux/Unix system.

The cdw 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 ls6 – 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
$WORK - Refers to a sub-directory of the shared Work area that is different for different clusters, e.g.:
- /work/01063/abattenh/lonestarls6 on ls5 lonestar6
- /work/01063/abattenh/stampede2 on stampede2

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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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ls /corral-repl/utexas/BioITeam

A couple of things to keep in mind regarding corral:

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ranch is a gigantic (multiple PB) tape archive system where researchers can archive data. All TACC users have an automatice automatic 2 TB ranch allocation. UT researchers may request larger (multi-TB) ranch storage allocations through the normal TACC allocation request process.

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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 ls6 clusters. So remote copy commands are always needed to copy data to and from ranch (e.g. scp, rsync).

Staging your data

So, your sequencing center has some data for you. They may send you a list of web or FTP links to use to download the data.

The first task is to get this sequencing data to a permanent storage area. This should not be your laptop! corral (or stockyard) is a great place for it, or a server maintained by your lab or company.

Here's an example of a "best practice". Wherever your permanent storage area is, it should have a rational sub-directory structure that reflects its contents. It's easy to process a few NGS datasets, but when they start multiplying like tribbles, good organization and naming conventions will be the only thing standing between you and utter chaos!

For example:

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 – 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.

Download from a link – wget

Well, you don't have a desktop at TACC to "Save as" to, so what to do with a link? The wget program knows how to access web URLs such as http, https and ftp.

...

wget

Get ready to run wget from the directory where you want to put the data.

Don't press Enter after the wget command – just put a space after it.

Code Block

language	bash
title	Get ready to wget

mkdir -p $WORK/archive/original/2020.core_ngs
cd $WORK/archive/original/2020.core_ngs
wget

Here are two web links:

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About file systems

File systems are storage areas where files and directories are arranged in a hierarchy. Any computer can have one or more file systems "mounted" (accessible as local storage). The df command can be used on any Unix system to show all the "top-level" mounted file systems. TACC has a lot of temporary file systems, so lets just look at the first 15 and tell df to use "human readable" size formatting with the -h option:

Code Block

language	bash

df -h | head -15

The rightmost "Mounted on" column give the top-level access path. Find /home1, /work, and /scratch and note their sizes!

What do we mean by "hierarchy"? It is like a tree, with the root file system as the trunk, sub-directories as branches, sub-sub-directories as branches from branches (and so forth), with files as leaves off any branch.

your TACC Home directory
using home-directory-relative (~) path syntax

Image Added

But everyone has a Home directory, so you must only be seeing a part of the Home directory hierarchy. To see the absolute path of a directory you're in, use the pwd -P command. Note that absolute paths always start with a forward slash ( / ) denoting its root file system.

Code Block

language	bash

pwd -P
# will show something like this
# /home1/01063/abattenh

That shows you that your Home directory (~) is actually 3 levels down in the /home1 hierarchy:

part of the TACC Home file system
using absolute paths

Image Added

Here's a depiction of the three file systems as seen from your Home directory ( ~ ), showing where the path-valued environment variables represent, and where the three symbolic links (~/CoreNGS, ~/scratch, ~/work) you created in your Home directory point. Notice that both the Work and Scratch file systems have a top-level hierarchy like we saw in Home above.

Image Added

Staging your data

So, your sequencing center has some data for you. They may send you a list of web or FTP links to use to download the data.

The first task is to get this sequencing data to a permanent storage area. This should not be your laptop! corral (or stockyard) is a great place for it, or a server maintained by your lab or company.

Here's an example of a "best practice". Wherever your permanent storage area is, it should have a rational sub-directory structure that reflects its contents. It's easy to process a few NGS datasets, but when they start multiplying like tribbles, good organization and naming conventions will be the only thing standing between you and utter chaos!

For example:

original – for original sequencing data (compressed FASTQ files)
- sub-directories named, for example, by year_month.<sequencing run/job or project name>
aligned – for alignment data (BAM files, etc)
- sub-directories named, e.g., by year_month.<project_name>
analysis – further downstream analysis
- reasonably named sub-directories, often by project
refs – reference genomes and other annotation files used in alignment and analysis
- sub-directories for different reference genomes and aligners
- e.g. ucsc/hg38/star, ucsc/sacCer3/bwa, mirbase/v20/bowtie2
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.
- can have separate sub-directories for people, or various shared repositories.

Download from a link – wget

Well, you don't have a desktop at TACC to "Save as" to, so what to do with a link? The wget program knows how to access web URLs such as http, https and ftp.

Anchor

	wget yeast data
	wget yeast data

wget

Get ready to run wget from the directory where you want to put the data.

Don't press Enter after the wget command – just put a space after it.

Code Block

language	bash
title	Get ready to wget

mkdir -p $SCRATCH/archive/original/2021.core_ngs
cd $SCRATCH/archive/original/2021.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

language	bash
title	wget to retrieve a web URL

wget http://web.corral.tacc.utexas.edu/

...

BioinformaticsResource/CoreNGS/yeast_stuff/Sample_Yeast_L005_

...

R1.cat.fastq.gz

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:

...

language	bash
title	wget to retrieve a web URL

...

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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The cp command copies one or more files from a local source to a local destination. It has many options, but the most common form is:

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

language	bash
title	Single 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   # use the symbolic link in your Home directory
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

language	bash
title	Directory copy with cp

mkdir -p $SCRATCH/data 
cds
cd data
cp -r $CORENGS/general/ general/

Exercise: What files were copied over?

Expand

title	Hint

ls ls general
# or
tree $SCRATCH/data/general

Expand

title	Answer

BEDTools-User-Manual.v4.pdf  SAM1.pdf  SAM1.v1.4.pdf

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rsync is a very complicated program, with many options (http://rsync.samba.org/ftp/rsync/rsync.html). However, if you use the recipe shown here for directories, it's hard to go wrong:

rsync -avW local/path/to/source_directory/ local/path/to/destination_directory/

Both the source and target directories are local (in some file system accessible directly from ls5 lonestar6). 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).

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Tip

title	Always add a trailing slash ( / ) after directory names

The trailing slash ( / ) on the source and destination directories are very important for rsync (and for other Linux copy commands also)!

rsync will create the last directory level for you, but earlier levels must already exist.

...

Code Block

language	bash
title	rsync (local directory)

mkdir -p $SCRATCH/data
cds
rsync -avWPavrW $CORENGS/custom_tracks/ data/custom_tracks/

...

Expand

title	Hint

ls $SCRATCH/data/custom_tracks
# or
ls ~/scratch/data/custom_tracks
# or
cds; cd data/custom_tracks; ls
# or
tree $SCRATCH/data

Now repeat the rsync and see the difference.

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Code Block

language	bash

rsync -avWPavrW /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; Ctrl-e to the enduse Backspace to remove text before the cursor; Delete to remove text after the cursorDeleteto remove text after the cursor
Ctrl-k ("kill") to delete all text on your command line after the cursor
Ctrl-y ("yank") to copy the last killed text to where the cursor is

Copy from a remote computer - scp or rsync

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Code Block

title	single remote file copy with scp

mkdir -p $SCRATCH/data/test1
cds
cat $CORENGS/tacc/dragonfly_access.txt
cds
mkdir -p data/test2
scp corengstools@dragonfly.icmb.utexas.edu:~/custom_tracks/progeria_ctcf.vcf.gz ./data/test1test2/
lstree .$SCRATCH/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

...

The tilde ( ~ ) at the start of the path means "relative to my home directory"
We use the tilde ( ~ ) in the destination to traverse the ~/scratch symbolic link in your home directory.

Code Block

language	bash
title	rsync (remote directory)	rsync (remote directory)

cat $CORENGS/tacc/dragonfly_access.txt
rsync -avWPavrW corengstools@dragonfly.icmb.utexas.edu:~/custom_tracks/ ~/scratch/data/custom_tracks/

...

Expand

title	Answer

No, because all the source files were already present in the destination directory (you copied the same files earlier) with the same names, file sizes and timestamps. So rsync had nothing to do!

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Here's a fun scavenger hunt for more practice . Issue of the following commands to get practice what you've learned so far:.

Expand

title	Hint

Hit Tab Tab as much as possible to save typing!

To get started:

...

title	Play a scavenger hunt for more practice

...

started:

Code Block

title	Play a scavenger hunt for more practice

cd
cp -r /work/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

title	Answer

ls5ls6:~/what/starts/here/changes/the/world

...

Expand

title	Step 2 answer

From inside your ~/what/starts directory:

Code Block

title	Play a scavenger hunt for more practice

mkdir here
cd here
wget http://web.corral.tacc.utexas.edu/BioinformaticsResource/BioITeamCoreNGS/step3.txt
cat step3.txt

Expand

title	Step 3 answer

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

Code Block

title	Play a scavenger hunt for more practice

scp -r /work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes/ changes/
# or
rsync -ptrvP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes/ changes/
# Note: rsync -avPavrP ... 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

...

Expand

title	Step 4 answer

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

Code Block

title	Play a scavenger hunt for more practice

rsync -avPavrP corengstools@dragonfly.icmb.utexas.edu:~/the/ the/
# or
scp -r corengstools@dragonfly.icmb.utexas.edu:~/the/ the/

cd the
cat instr5.txt
cd world
cat instr6.txt

The path to the directory you're in now should be:

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

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Versions Compared

Old Version 19

New Version Current

Key

Local file systems

changing TACC file systems

Staging your data

Download from a link – wget

wget

About file systems

Staging your data

Download from a link – wget

wget

Copy from a corral location - cp or rsync

Copy from a remote computer - scp or rsync