...
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 (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:
Home | Work | Scratch | |
---|---|---|---|
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 | cdw | cds |
environment variable | $HOME | $WORK (different sub-directory for each cluster) $STOCKYARD (root of the shared Work file system) $WORK (different sub-directory for each cluster) | $SCRATCH |
root file system | /home | /work | /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 |
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--------------------- Project balances for user abattenh ---------------------- | Name Avail SUs Expires | Name Avail SUs Expires | | OTH21095 genomeAnalysis 673 2021-03-31 |1000 BioinformaticsResour 100 2020-062022-09-30 | | UT-2015-05-18 MCB21106 1000 2021-03-31 | DNAdenovo 995 2022-12-31 | | OTH21164 4969 2021-03-31 | | CancerGenetics 1000 4856 2020-09-302022-12-31 | A-cm10OTH21037 4224 8867 20202022-12-31 | ------------------------ Disk quotas for user abattenh ------------------------ | Disk Usage (GB) Limit %Used File Usage Limit %Used | | /home1 0.0 1011.07 0.1000 52 153 10000000 0.0200 | | /work 614169.50 1024.0 6016.0150 6109479362 3000000 2.04 | | /scratch 2676.6 0.0 0.00 32442 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.
...
Tip |
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The cd (change directory) command with no arguments takes you to your home directory on any Linux/Unix system. The cdw 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 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
- 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
...
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 | ||||
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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 automatic 2 TB ranch allocation. UT researchers may request larger (multi-TB) ranch storage allocations through the normal TACC allocation request process.
...
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! 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
- 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.
...
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 | ||
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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 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.
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 its root file system.
Code Block | ||
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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.
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.
Anchor | ||||
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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.
Code Block | ||||
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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:
Code Block | ||||
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| ||||
wget |
...
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.
Code Block | ||||
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| ||||
mkdir -p $WORK/archive/original/2020.core_ngs
cd $WORK/archive/original/2020.core_ngs
wget |
Here are two web links:
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).
Tip |
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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. |
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.
Code Block | ||||
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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 # 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"
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 | ||||
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| ||||
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 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 scratch area and copy a single file to it. The trailing slash ( / ) on the destination says it is a directory.
Code Block | |||||
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mkdir -pmkdir -p $SCRATCH/data/test1 cp $CORENGS/misc/small.fq $SCRATCH/data/test1/ ls $SCRATCH/data/test1 cds #cd or..data mkdircp -pr ~$CORENGS/scratchgeneral/data/test1 cd ~/scratch/data/test1 cp $CORENGS/misc/small.fq . ls |
Copy an entire directory to your scratch area. The -r argument says "recursive".
Code Block | ||||
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mkdir -p $SCRATCH/data
cds
cd data
cp -r $CORENGS/general/ general/ |
Exercise: What files were copied over?
Expand | ||
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ls general |
Expand | ||
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| ||
BEDTools-User-Manual.v4.pdf SAM1.pdf SAM1.v1.4.pdf |
local rsync
...
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). Either full or relative path syntax can be used for both. The -avP options above stand for:
...
- -p – preserve file permissions
- -t – preserve file times
- -l – copy symbolic links as links
- -r – recursively copy sub-directories
general/ |
Exercise: What files were copied over?
Expand | ||
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| ||
ls general |
Expand | ||
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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".
Tip | ||
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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. |
Code Block | ||||
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| ||||
mkdir -p $SCRATCH/data
cds
rsync -avrW $CORENGS/custom_tracks/ data/custom_tracks/ |
Exercise: What files were copied over?
Expand | ||
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| ||
ls $SCRATCH/data/custom_tracks |
Now repeat the rsync and see the difference.
Use the Up arrow to retrieve the previous command from your bash command history
...
- 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".
...
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)!
...
.
Code Block | |||
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rsync | (local directory)mkdir -p $SCRATCH/data cds rsync -avWP $CORENGSavrW /work/projects/BioITeam/projects/courses/Core_NGS_Tools/custom_tracks/ data/custom_tracks/ |
Exercise: What files were copied over?
Expand | ||
---|---|---|
| ||
ls $SCRATCH/data/custom_tracks |
Now repeat the rsync and see the difference.
Use the Up arrow to retrieve the previous command from your bash command history.
Code Block | ||
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| ||
rsync -avWP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/custom_tracks/ data/custom_tracks/ |
Tip |
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The bash shell has several convenient line editing features:
|
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)
Code Block | ||
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| ||
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.
Code Block | ||||
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| ||||
rsync -ptlrvP corengstools@gapdh.icmb.utexas.edu:~/custom_tracks/ ~/scratch/data/custom_tracks/ |
Exercise: Was anything copied?
Expand | ||
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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 timestamps and file checksums. So rsync had nothing to do! |
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:
Expand | ||
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| ||
Hit Tab Tab as much as possible to save typing! |
...
Tip |
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The bash shell has several convenient line editing features:
|
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)
Code Block | ||
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| ||
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.
Code Block | ||||
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| ||||
cat $CORENGS/tacc/dragonfly_access.txt
rsync -avrW corengstools@dragonfly.icmb.utexas.edu:~/custom_tracks/ ~/scratch/data/custom_tracks/ |
Exercise: Was anything copied?
Expand | ||
---|---|---|
| ||
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! |
Scavenger hunt exercise
Here's a fun scavenger hunt for more practice of the commands you've learned so far.
Expand | ||
---|---|---|
| ||
Hit Tab Tab as much as possible to save typing! |
To get started:
Code Block | ||
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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?
Expand | ||
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|
step by step answers
Expand | |||||
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From inside your ~/what directory:
|
Expand | |||||
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From inside your ~/what/starts directory:
|
Expand | ||||
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| ||||
From inside your ~/what/starts/here directory:
| ||||
cd
cp -r $CORENGS/linuxpractice/what what
cd what
cat readme |
Where are you when you're all done?
Expand | ||
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| ||
|
step by step answers
Expand | |||||
---|---|---|---|---|---|
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From inside your ~/what directory:
|
Expand | |||||
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From inside your ~/what/starts directory:
|
Expand | |||||
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From inside your ~/what/starts/here directory:
|
...
Expand | |||||
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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 |