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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 |
|---|
| language | bash |
|---|
| title | Our shared class directory |
|---|
|
ls /work/projects/BioITeam/projects/courses/Core_NGS_Tools |
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| Code Block |
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| language | bash |
|---|
| title | Single file copy with cp |
|---|
|
mkdir -p $SCRATCH/data/test1
cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/$CORENGS/misc/small.fq $SCRATCH/data/test1/
ls $SCRATCH/data/test1
# or..
mkdir -p ~/scratch/data/test1
cd ~/scratch/data/test1
cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/$CORENGS/misc/small.fq .
ls |
Copy an entire directory to your scratch area. The -r argument says "recursive".
| Code Block |
|---|
| language | bash |
|---|
| title | Directory copy with cp |
|---|
|
cds
cd data
cp -r /work/projects/BioITeam/projects/courses/Core_NGS_Tools/$CORENGS/general/ general/ |
Exercise: What files were copied over?
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Both the source and target directories are local (in some file system accessible directly from ls5). Either full or relative path syntax can be used for both. The -ptlrvPavP options above stand for:
- -a means "archive mode", which implies the following options (and a few others)
- -p – preserve file permissions
- -t – preserve file times
- -l – copy symbolic links as links
- -r – recursively copy sub-directories
- -v means verbose
- -P means show Progress.
Since these are all single-character options, they can be combined after one option prefix dash ( - ). You could also use options -ptlrvP, separately, instead of using -a for "archive mode".
| Tip |
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| title | Always add a trailing slash ( / ) after directory names |
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|
The trailing slash ( / ) on the source and destination directories are very important! rsync will create the last directory level for you, but earlier levels must already exist. |
| Tip |
|---|
| title | Use -W option when transferring large files |
|---|
|
Another useful option is -W (copy Whole files only). In its normal mode, rsync will copy only changed parts of newer files. For large files, figuring out what has changed (diff-ing) can take more time than just copying the whole file. The rsync -W option says to skip diff-ing. |
| Code Block |
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| language | bash |
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| title | rsync (local directory) |
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|
cds
rsync -avP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/$CORENGS/custom_tracks/ data/custom_tracks/ |
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| Code Block |
|---|
| title | Play a scavenger hunt for more practice |
|---|
|
cd
cp -r /work/projects/BioITeam/projects/courses/Core_NGS_Tools$CORENGS/linuxpractice/what what
cd what
cat readme |
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