Page History

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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

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:

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

--------------------- Project balances for user abattenh ----------------------
| Name           Avail SUs     Expires  | Name           Avail SUs     Expires |
| CancerGeneticsOTH21095            48561000  20182022-09-30 | A-cm10MCB21106             995 1096  20182022-12-31 |
| UT-2015-05-18OTH21164            21001000  20192022-0312-31 | genomeAnalysisOTH21037            25004224  20192022-0312-31 |
------------------------ Disk quotas for user abattenh -------------------------
| Disk         Usage (GB)     Limit    %Used   File Usage       Limit   %Used |
| /home1              0.0      1011.07     0.1200           52  91     1000000    0.01 |    0.00 |
| /work             538169.50    1024.0    5216.5950        6105379362     3000000    2.04 |
| /scratch         3725.9       0.0     0.00         4137           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.

...

...

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.

...

• $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

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.

...

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 /work/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.

ls /corral-repl/utexas/BioITeam

A couple of things to keep in mind regarding corral:

A couple of things to keep in mind regarding corral:

• corral is 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!

...

ranch is a gigantic (multiple PB) tape archive system where researchers can archive data. All TACC users have an automatic 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 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 or one of the TACC local file systems! corral is a great place for it, or a server maintained by your lab or company.

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:We're going to pretend – just for the sake of this class – that your permanent storage area is in your TACC work area. Execute these commands to make your "archive" directory and some sub-directories.

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 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 by year_month.<project_name>
• aligned – for alignment artifacts (bam files, etc)
  • sub-directories named by year_month.<project_name>
• analysis – further downstream analysis
  • reasonably named subdirectories, 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.

cd $WORK/archive/original/2018_05.core_ngs
wget 

Here are two web links:

• http://web.corral.tacc.utexas.edu/BioITeam/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
• http://web.corral.tacc.utexas.edu/BioITeam/yeast_stuff/Sample_Yeast_L005_R2.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:

wget http://web.corral.tacc.utexas.edu/BioITeam/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/misc/small.fq  $SCRATCH/data/test1/
ls $SCRATCH/data/test1

# or..
mkdir -p ~/scratch/data/test1
cd ~/scratch/data/test1
cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small.fq  .
ls

Copy an entire directory to your scratch area. The -r argument says "recursive".

cds
cd data
cp -r /work/projects/BioITeam/projects/courses/Core_NGS_Tools/general/ general/

Exercise: What files were copied over?

ls general

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

local rsync

...

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.

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.

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:

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.

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.

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

Here are two web links:

• https://web.corral.tacc.utexas.edu/BioinformaticsResource/CoreNGS/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
• https://web.corral.tacc.utexas.edu/BioinformaticsResource/CoreNGS/yeast_stuff/Sample_Yeast_L005_R2.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:

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

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 area. The -r option says "recursive".

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

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

• -p means preserve file permissions
• -t means preserve file times
• -l means copy symbolic links as links
• -r means recursively copy sub-directories
• -v means verbose
• -P means show Progress.

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

cds
rsync -ptlrvP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/ucsc_custom_tracks/ data/custom_tracks/

Exercise: What files were copied over?

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

Now repeat the rsync and see the difference.

Use the Up arrow to retrieve the previous command from your bash command history.

rsync -ptlrvP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/ucsc_custom_tracks/ data/custom_tracks/

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.

The good news is that once you have learned cp and local rsync, remote secure copy (scp) and remote rsync are very similar!

scp

The scp command copies one or more files from a source to a destination, where either source or destination, or both, can be a remote path.

Remote paths are similar to local paths, but have user and host information first:

user_name@full.host.name:/full/path/to/directory/or/file

– or –

user_name@full.host.name:~/path/relative/to/home/directory

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

cds
cat $CORENGS/tacc/gapdh_access.txt
scp corengstools@gapdh.icmb.utexas.edu:~/custom_tracks/progeria_ctcf.vcf.gz ./data/test1/
ls ./data/test1

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

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 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.

general

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

local rsync

The rsync command is typically used to copy whole directories. What's great about rsync is that itonly copies what has changed in the source directory. So if you regularly rsync a large directory to TACC, it may take a long time the 1st time, but the 2nd time (say after downloading more sequencing data to the source), only the new files will be copied.

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 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).

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".

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

rsync -ptlrvP corengstools@gapdh.icmb.utexas.edu:~/custom_tracks/ ~/scratch/data/custom_tracks/

Exercise: Was anything What files were copied over?

Scavenger hunt exercise

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

To get started:

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.

Use the Up arrow to retrieve the previous command from your bash command history.

rsync -avrW /work/projects

cd
cp -r /work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpracticecustom_tracks/what what
cd what
cat readme

Where are you when you're all done?

step by step answers

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

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

 data/custom_tracks/

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.

The good news is that once you have learned cp and local rsync, remote secure copy (scp) and remote rsync are very similar!

scp

The scp command copies one or more files from a source to a destination, where either source or destination, or both, can be a remote path.

Remote paths are similar to local paths, but have user and host information first:

user_name@full.host.name:/full/path/to/directory/or/file

– or –

user_name@full.host.name:~/path/relative/to/home/directory

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

cat $CORENGS/tacc/dragonfly_access.txt
cds
mkdir -p data/test2
scp corengstools@dragonfly.icmb.utexas.edu:~/custom_tracks/progeria_ctcf.vcf.gz ./data/test2/
tree $SCRATCH/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
• The  -r recursive argument works for scp also, just like for cp

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 directory"
• We use the tilde ( ~ ) in the destination to traverse the ~/scratch symbolic link in your home directory.
  
  

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

Exercise: Was anything copied?

Scavenger hunt exercise

Here's a fun scavenger hunt for more practice of the commands you've learned so far.

To get started:

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?

step by step answers

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

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

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 -avrP ... 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.
 

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

# Then
cd changes 
more largeFile.txt

rsync -ptlrvP corengstools@gapdhavrP 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