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  • wget – retrieves the contents of an Internet URL
  • cp – copies files located on any local file system
  • scp – copies files to/from a remote system
  • rsync – copies directories or files on either local or remote systems
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 TB122+ 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).

When you first login, the system gives you information about disk quota and your compute allocation quota:

Code Block
--------------------- Project balances for user abattenh ----------------------
| Name           Avail SUs     Expires  | Name           Avail SUs     Expires |
| CancerGeneticsgenomeAnalysis       4856673  20182021-0903-3031 | A-cm10BioinformaticsResour 100             1096  2018-12-312020-06-30 |
| UT-2015-05-18       21001000  20192021-03-31 | DNAdenovo genomeAnalysis      2500  2019  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     0.1210           91153     1000000    0.0102 |
| /workwork2             538614.5    1024.0    5260.5901        6105361094     3000000    2.04 |
| /scratch         37252676.96       0.0     0.00         413732442           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.

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.

...

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)
  • $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

A mechanism 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
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
lsecho $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.

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

A couple of things to keep in mind regarding corral:

...

ranch is a gigantic (multiple PB) tape archive system where researchers can archive data. All TACC users have an automatice 2 TB ranch allocation. UT researchers may request large 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 "staged". See the ranch user guide for more information: https://www.tacc.utexas.edu/user-services/user-guides/ranch-user-guide.

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).

...

The first task is to get this sequencing data to a permanent storage area. This should not be your laptop or one of the TACC local file systems! corral (or stockyard) is a great place for it, or a server maintained by your lab or company.We're going

to pretend – just for the sake of this class – that Here's an example of a "best practice". Wherever your permanent storage area is in your TACC work area. Execute these commands to make your "archive" directory and some sub-directories.

Code Block
languagebash
titleCreate a pretend "archive" directory
mkdir -p $WORK/archive/original/2018_05.core_ngs

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 , 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 FASTQ files)
    • sub-directories named, for example, by year_month.<project_name>
  • aligned – for alignment artifacts (bam BAM files, etc)
    • sub-directories named, e.g.,  by year_month.<project_name>
  • analysis – further downstream analysis
    • reasonably named subdirectoriessub-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.

...

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
languagebash
titleGet ready to wget
cd $WORKmkdir -p $SCRATCH/archive/original/2018_052021.core_ngs
wget 

...

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
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).

Copy from a corral location - cp or rsync

Suppose you have a corral allocation where your organization keeps its data, and that the sequencing data has been downloaded there. You can use various Linux commands to copy the data locally from there to your $SCRATCH area.

cp

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

cp [options] <source file 1> <source file 2> ... <destination directory>/

Make a directory in your scratch area and copy a single file to it. The trailing slash ( / ) on the destination says it is a directory.

mkdir -p $SCRATCH/data/test1 cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools
Code Block
languagebash
titleSingle file copy with cp
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

Suppose you have a corral allocation or stockyard area where your organization keeps its data, and that the sequencing data has been downloaded there. You can use various Linux commands to copy the data locally from there to your $SCRATCH area.

cp

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

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
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/work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small.fq 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 $SCRATCH/data
cds
cd data
cp -r /work/projects/BioITeam/projects/courses/Core_NGS_Tools/$CORENGS/general/ general/

Exercise: What files were copied over?

...

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 -ptlrvP 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 stampede2). Either full or relative path syntax can be used for both. The -ptlrvPavW options above stand for:

  • -p means preserve file permissions-t means a means "archive mode", which implies the following options (and a few others)
    • -p – preserve file permissions
    • -t preserve file times
    • -l
    means
    • copy symbolic links as links
    • -r
    means
    • recursively copy sub-directories
  • -v means verbose
  • -P means show Progress.

...

  • 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).

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

Tip
titleAlways 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
languagebash
titlersync (local directory)
mkdir -p $SCRATCH/data
cds
rsync -ptlrvP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/ucsc_avW $CORENGS/custom_tracks/ data/custom_tracks/

...

Code Block
languagebash
rsync -ptlrvPavW /work/projects/BioITeam/projects/courses/Core_NGS_Tools/ucsc_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

Provided that the remote computer is running Linux and you have ssh access to it, you can use various Linux commands to copy data over a secure connection.

...

Copy a single file to your $SCRATCH/data/test1 directory from the server named gapdhdragonfly.icmb.utexas.edu, using the user account corengstools. When prompted for a password, use the one we have written on to the board Zoom chat (or copy/paste the password from this file: $CORENGS/tacc/gapdhdragonfly_access.txt)

Code Block
titlesingle remote file copy with scp
cds
cat $CORENGS/tacc/gapdhdragonfly_access.txt
cds
mkdir -p data/test2
scp corengstools@gapdhcorengstools@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

...

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

Don't forget to change userid below.

...



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

...

Expand
titleAnswer

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

...

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

Expand
titleHint

Hit Tab Tab as much as possible to save typing!

To get started:

Code Block
titlePlay a scavenger hunt for more practice
cd
cp -r /work2/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

stamp2:~/what/starts/here/changes/the/world

step by step answers

Expand
titleHint

Hit Tab Tab as much as possible to save typing!

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Step 1 answer

From inside your ~/what directory:

Code Block
titlePlay a scavenger hunt for more practice
cd
mkdir starts
cd starts
cp 
-r
/
work
work2/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/steps/
what what cd what
nextInstr .
cat 
readme

Where are you when you're all done?

nextInst
Expand
titleAnswer

ls5:~/what/starts/here/changes/the/world

...

Step 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/BioinformaticsResource/CoreNGS/step3.txt
cat step3.txt
Expand
titleStep 2 3 answer

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

mkdir starts cd starts cp /work
Code Block
titlePlay a scavenger hunt for more practice
scp -r /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes/ changes/
# or
rsync -ptrvP /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes/steps/nextInstr .
cat nextInst
Expand
titleStep 3 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/BioITeam/step3.txt
cat step3.txt
Expand
titleStep 4 answer

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

Code Block
titlePlay a scavenger hunt for more practice
rsync -ptlrvP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes/ changes/
# or
scp -r scp -r /work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes 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
Expand
titleStep 5 4 answer

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

Code Block
titlePlay a scavenger hunt for more practice
rsync -ptlrvP corengstools@gapdhavP 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

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