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

Local file systems

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:

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 |
| genomeAnalysisOTH21095           67327688  20212025-0301-31 | DNAdenovo BioinformaticsResour 100  2020-06-30 | | UT-2015-05-18    3000   1000  2021-03-312024-09-30 |
| DNAdenovoOTH21164            49691010  20212025-03-31 | | CancerGenetics      4856OTH21180  2020-09-30 | A-cm10         996     8867  2020-122025-03-31 |
------------------------ Disk quotas for user abattenh ------------------------ 
| Disk         Usage (GB)     Limit    %Used   File Usage       Limit   %Used |
| /home1scratch              0.0       100.0     0.1000          153  0   1000000    0.02 |
   0    0.00 |
| /work2home1              6140.50      1024.011.7     0.02        60.01  316      61094     30000000    20.0400 |
| /scratchwork         2676.6       0169.0     1024.0.00    16.50    32442    79361     3000000  0  2.65 |
0.00 |
------------------------------------------------------------------------------- 

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.

cdw2
cds
cdcdw    # cd $WORK
cds    # cd $SCRATCH
cd     # cd $HOME

...

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)
    
• $WORK2 $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/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.

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.

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.

The UT/Austin BioInformatics Team also has an older, common directory area on corral.

...

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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

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
• 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.

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.

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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 $WORK2/archive/original/2021.core_ngs
cd $WORK2/archive/original/2021.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:

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!

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.

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.

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

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 be your laptop! corral (or stockyard) is a great place for it, a BRCF pod, 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.
  • 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.

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/2024.core_ngs
cd $SCRATCH/archive/original/2024.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

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:

...

...

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

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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.

mkdir -p $SCRATCH/data/test1
cp $CORENGS/misc/small.fq  $SCRATCH/data/test1/
ls $SCRATCH/data/test1

# or..
cds
mkdir -p $SCRATCH/ -p data/test1
cd 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 (Read more about using Absolute or Relative pathname syntax)

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

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

Exercise: What files were copied over?

ls general
# or
tree $SCRATCH/data

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).
    • 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".

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

mkdir -p $SCRATCH/data
cds
rsync -avWPavW -P $CORENGS/custom_tracks/ data/custom_tracks/

...

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

Now repeat the rsync and see the difference.

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rsync -avWPavrW /work/projects/BioITeam/projects/courses/Core_NGS_Tools/custom_tracks/ data/custom_tracks/

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Copy from a remote computer - scp or rsync

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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 -p corengstools@dragonfly.icmb.utexas.edu:~/custom_tracks/progeria_ctcf.vcf.gz ./data/test1test2/
lstree ./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
  • 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.
  
  

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

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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:.

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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?

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mkdir here
cd here
wget http://web.corral.tacc.utexas.edu/BioITeamBioinformaticsResource/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 -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

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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