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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) |
Local file systems
There are 3 local file systems available on any TACC compute cluster (stampede2, 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 | |||
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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 | 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).
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--------------------- Project balances for user abattenh ---------------------- | Name Avail SUs Expires | Name Avail SUs Expires | | genomeAnalysisOTH21095 673 2021-03-31 | BioinformaticsResour 100905 20202023-0609-30 | | UT-2015-05-18 MCB21106 1000 2021-03-31 |1496 DNAdenovo 2023-09-30 | | OTH21164 4969 2021-03-31 | | CancerGenetics 4856215 20202024-0905-3031 | A-cm10OTH21180 899 8867 20202024-1203-31 | ------------------------ Disk quotas for user abattenh ------------------------ | Disk Usage (GB) Limit %Used File Usage Limit %Used | | /home1 scratch 0.07 100.0 0.1000 567 153 1000000 0.02 | | /work2 0.00 | | /home1 6140.50 102411.07 600.01 61094 232 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.
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cdw2 cds cdcdw # cd $WORK cds # cd $SCRATCH cd # cd $HOME |
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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 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)
- 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/stampede2 on stampede2
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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.
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echo $CORENGS ls /work2work/projects/BioITeam/projects/courses/Core_NGS_Tools |
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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).
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:
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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!
What do we mean by "hierarchy"? It 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 |
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.
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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 |
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.
On many Linux systems, you can use the tree command to view the full file system hierarchy starting from a specified directory:
Staging your 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.
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- 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/hg38/hg19star, 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. Anchor
wget
Get ready to run wget from the directory where you want to put the data.
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mkdir -p $WORK2$SCRATCH/archive/original/2021.core_ngs cd $WORK2$SCRATCH/archive/original/2021.core_ngs wget |
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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:
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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 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.
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mkdir -p $SCRATCH/data/test1 cp $CORENGS/misc/small.fq $SCRATCH/data/test1/ ls $SCRATCH/data/test1 # or.. mkdir -p ~/scratch/data/test1.. 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 |
(Read more about using Absolute or Relative pathname syntax)
Now copy Copy an entire directory to your scratch Scratch area. The -r argument says "recursive" option says recursive.
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mkdir -p $SCRATCH/data
cds
cd data
cp -r $CORENGS/general/ general/ |
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ls general |
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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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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. |
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mkdir -p $SCRATCH/data cds rsync -avWPavrW $CORENGS/custom_tracks/ data/custom_tracks/ |
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ls $SCRATCH/data/custom_tracks |
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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Tip |
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The bash shell has several convenient line editing features:
Once the cursor is positioned where you want it:
(Read more about Command line history and editing) |
Copy from a remote computer - scp or rsync
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mkdir -p $SCRATCH/data/test1 cds 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 the ~/scratch symbolic link created in your home directory.
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cat $CORENGS/tacc/dragonfly_access.txt rsync -avWPavrW corengstools@dragonfly.icmb.utexas.edu:~/custom_tracks/ ~/scratch/data/custom_tracks/ |
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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:.
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Hit Tab Tab as much as possible to save typing! |
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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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From inside your ~/what/starts directory:
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From inside your ~/what/starts/here directory:
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From inside your ~/what/starts/here/changes directory:
The path to the directory you're in now should be: ~/what/starts/here/changes/the/world |