Command List

General Linux Commands

Moving around in the file system

Command	Action
pwd	"Print working directory" - show what directory you are in.
ls	List the contents (files and subdirectories) of a directory.
ls -l	List the contents of a dir and show additional info of the files.
ls -a	List all files, including hidden files, which typically start with a dot.
ls -lh	List the contents of a dir and show additional info of the files (the files sizes are given in easy to read units).
ls -lt	List the contents of a dir in cronological order with most recent files on top and show additional info of the files.
cd dirname	Change to the dirname directory.
cd ..	Go to the top level of your home directory.

Examining files

Command	Action
file filename	Determine the type of a file.
cat filename	Concatenate a file.
less filename	View text files and paginate them if needed.
more filename	View text files, one page at a time.

Manipulating files and directories

Command	Action
cp filename dirname	Copy a file into a directory.
cp filename1 filename2	Copy a file into another.
cp -i filename dirname	Copy a file into a directory and ask before overwriting.
cp -i filename1 filename2	Copy a file into another and ask before overwriting.
cp -r dir1 dir2	Copy a directory with its contents.
mv filename dirname	Move a file into a directory.
mv filename1 filename2	Renames a file.
mv -i filename dirname	Move a file and ask before overwriting.
mv -i filename1 filename2	Rename a file and ask before overwriting.
rm filename	Remove a file.
rm -r dirname	Remove a directory with its contents.
rm -i filename	Ask before removing a file.
rm -i -r dirname	Ask before removing a directory and its contents.
mkdir dirname	Make a directory.
rmdir dirname	Remove an empty directory.

Converting files to Linux format

Command	Action
dos2unix filename	Removes DOS/Windows line endings in file.
mac2unix filename	Removes Mac line endings in file.

zcluster specific commands

Command	Action
quotarep	Reports how much space you are using on the file systems
make_escratch	Creates an ephemeral scratch directory, which is delete after 38 days (all contents will be deleted)

SGE commands

Command	Action
qsub	Submit a job to the queue
qdel	Cancel a queued or running job
qhold	Place a queued job on hold
qstat	Check the status of queued and running jobs
qacct	List properties of finished jobs
qstat -g c	List all valid queue names