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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 -ptlrvP avP 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 a means "archive mode", which implies the following options (and a few others)
  
  • -p – 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 ptlrvP, separately, instead of using -a means for "archive mode", which implies the -ptl options.

cds
rsync -ptlrvPavP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/custom_tracks/ data/custom_tracks/

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

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rsync -ptlrvPavP /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 -ptlrvPavP corengstools@gapdh.icmb.utexas.edu:~/the/ the/
cd the
cat instr5.txt
cd world
cat instr6.txt

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