Page Comparison

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wget – retrieves the contents of an Internet URL
cp – copies directories or files located on any local file system
scp – copies directories or files to/from a remote system
rsync – copies directories or files on either local or remote systems

Read more about Copying files and directories

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)

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There are 3 local file systems available on any TACC compute cluster (stampede2stampede3, lonestar5 lonestar6, etc.), each with different characteristics. All these local file systems are very and your account has a directory in each of the three.

The 3 file local systems have different characteristics, but all are fast and set up for parallel I/O (Lustre file system).

On stampede2 lonestar6 these local file systems have the following characteristics:

	Home	Work2Work	Scratch
quota	10 GB	1024 GB = 1 TB	2+ PB (basically infinite)none
policy	backed up	not backed up, not purged	not backed up, purged if not accessed recently (~10 days)
access command	cd	cdw2cdw	cds
environment variable	$HOME	$WORK (different sub-directory for each cluster) $STOCKYARD (root of the *shared* Work file system) $WORK2 (different sub-directory for each cluster)	$SCRATCH	$SCRATCH
root file system	/home	/work2work	/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 | BioinformaticsResour27688 100  20202025-0601-3031 | | UT-2015-05-18DNAdenovo        1000  2021-03-31 |3000 DNAdenovo 2024-09-30 |
| OTH21164       4969  2021-03-31 | | CancerGenetics1010      4856  2020-09-302025-03-31 | A-cm10OTH21180             996 8867  20202025-1203-31 |
------------------------ Disk quotas for user abattenh ------------------------ 
| Disk         Usage (GB)     Limit    %Used   File Usage       Limit   %Used |
| /home1scratch              0.0      10 0.0     0.1000            0      153     10000000    0.0200 |
| /work2home1              6140.50    1024.0  11.7     0.02    60.01      316      61094     30000000    20.0400 |
| /scratchwork         2676.6       0169.0     1024.0.00    16.50    32442    79361     3000000  0    02.0065 |
-------------------------------------------------------------------------------

changing TACC file systems

When you first login, you start in your home Home directory. Use the cd, cdw2 cdw and cds commands to change to your other file systems. Notice how your command prompt helpfully changes to show your location.

Code Block

language	bash
title	Changing file systems at TACC

cdw2
cds
cd

Tip

cdw    # cd $WORK
cds    # cd $SCRATCH
cd     # cd $HOME

Tip

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

The cdw2 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 to stampede2 stampede3 to ls5 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 (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/lonestarls6 on ls5 lonestar6
- /work2work/01063/abattenh/stampede2stampede3 on stampede2 stampede3

A mechanism is being developed for purchasing larger stockyard allocations (above the 1 TB basic quota) from TACC are in development.

The UT Austin BioInformatics Team, a loose group of bioinformatics researchers, maintains a common directory area on stockyard.

Code Block

language	bash
title	The shared BioITeam directory

ls /work2work/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

language	bash
title	Our shared class directory

echo $CORENGS
ls /work2work/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 ~$80~$43/TB/year. A couple See https://docs.tacc.utexas.edu/hpc/corral/

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.

There is currently no charge for ranch storage. However, since the data is stored on tape it is not immediately available – robots find and mount appropriate tapes when the data is requested, and it can take minutes to hours for the data to appear on disk. The metadata about your data – the directory structures and file names – is always accessible, but the actual data in the files is not on disk until unless "staged". See the ranch user guide for more information: https://wwwdocs.tacc.utexas.edu/user-services/user-guides/ranch-user-guidehpc/ranch/.

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 stampede3 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

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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 Size numbers!

Code Block

Filesystem                                           Size  Used Avail Use% Mounted on
devtmpfs                                             126G     0  126G   0% /dev
tmpfs                                                126G   43M  126G   1% /dev/shm
tmpfs                                                126G  4.1G  122G   4% /run
tmpfs                                                126G     0  126G   0% /sys/fs/cgroup
/dev/md127                                           150G   92G   59G  61% /
/dev/sda2                                           1014M  207M  808M  21% /boot
/dev/md126                                           284G   21G  264G   8% /tmp
/dev/md125                                           8.0G  4.3G  3.8G  54% /var
129.114.40.1:/admin                                  3.5T  714G  2.6T  22% /admin
129.114.40.7:/home1                                  7.0T  6.5T  504G  93% /home1
172.29.200.10@o2ib1172:172.29.200.11@o2ib1172:/work  6.8P  2.5P  4.3P  37% /work
129.114.52.169:/corral/main                           38P   21P   18P  55% /corral
tmpfs                                                 26G     0   26G   0% /run/user/891443
tmpfs                                                 26G     0   26G   0% /run/user/881379

What do we mean by "hierarchy"? The file system hierarchy is like a tree, with the root file system (denoted by the leading / ) 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 the 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

On many Linux systems, you can use the tree command to view the full file system hierarchy starting from a specified directory:

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 NOT be your laptop! corral (or stockyard) is a great place for it, a BRCF pod, or a server maintained by your lab or company.

...

original – for original sequencing data (compressed FASTQ files)
- sub-directories named, for example, by year_month.<project_<sequencing run/job or project name>
aligned – for alignment artifacts 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/hg19hg38/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.
- easiest to name 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.anchorwget yeast datawget yeast data

wget

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

...

Code Block

language	bash
title	Get ready to wget

mkdir -p $SCRATCH/archive/original/20212024.core_ngs
cd $SCRATCH/archive/original/20212024.core_ngs
wget

Here are two web links:

...

Now press Enter to get the command going. Repeat for the 2nd link. Check that you now see the two files (ls)., or tree $SCRATCH to see your Scratch directory hierarchy:

Image Added

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.

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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 Scratcharea and copy a single file to it. The trailing slash ( / ) on the destination says 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..
cds
mkdir -p data/test1
cd data/test1
cp $CORENGS/misc/small.fq .

# 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 (Read more about using Absolute or Relative pathname syntax)

Now copy an entire directory to your Scratch area. The -r option says "recursive" recursive.

Code Block

language	bash
title	Directory copy with cp

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

...

Expand

title	Hint

ls general
# or
tree $SCRATCH/data

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 stampede2 lonestar6). Either full or relative path syntax can be used for both. The -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).
Files are only copied if their modification date is more recent or the file size is different

Since these are all single-character options, they can be combined after one option prefix dash ( - ). You could also use options -ptlrvW, separately, instead of using -a for "archive mode".

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 existcreate the last directory level for you, but earlier levels must already exist.

Let's copy a directory using rsync. We'll also add the -P option to show Progress as the copy progresses.

Code Block

language	bash
title	rsync (local directory)

mkdir -p $SCRATCH/data
cds
rsync -avW -P $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 -avWavrW /work/projects/BioITeam/projects/courses/Core_NGS_Tools/custom_tracks/ data/custom_tracks/

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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 linecursor to the start of a line; Ctrl-e to the end
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

Once the cursor is positioned where you want it:

Just type in any additional text you want
To delete text after the cursor, use:
- Delete key on Windows
- Function-Delete keys on Macintosh
To delete text before the cursor, use:
- Backspace key on Windows
- Delete key on Macintosh

(Read more about Command line history and editing)

Copy from a remote computer - scp or rsync

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Code Block

title	single remote file copy with scp

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

Notes:

The 1st time you access a new host the SSH security prompt will appear
You will be prompted for your remote host password
for security reasons characters will not be echoed
The -r recursive argument works for scp also, just like for cp
The -p argument says to preserve the file's last modification time
otherwise the last modification time of the local copy will be when the copy was done

remote rsync

rsync can be run just like before, but using the remote-host syntax. Here we use two tricks:

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

Code Block

language	bash
title	rsync (remote directory)

cat $CORENGS/tacc/dragonfly_access.txt
rsync -avWavrW 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!

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Code Block

title	Play a scavenger hunt for more practice

cd
cp -r /work2work/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

stamp2ls6:~/what/starts/here/changes/the/world

...

Expand

title	Step 1 answer

From inside your ~/what directory:

Code Block

title	Play a scavenger hunt for more practice

mkdir starts
cd starts
cp /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/steps/nextInstr .
cat nextInst

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Expand

title	Step 3 answer

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

Code Block

title	Play a scavenger hunt for more practice

scp -r /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes/ changes/
# or
rsync -ptrvP /work2work/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

Versions Compared

Old Version 30

New Version Current

Key

changing TACC file systems

Staging your data

About file systems

Staging your data

Download from a link – wget

wget

Copy from a remote computer - scp or rsync

remote rsync