wiki

Bash

Permissions

With ACL (linux), you can use “getfacl” and “setfacl” to see and set permissions.

# See directory permissions
getfacl directory/name
getfacl: Removing leading '/' from absolute path names
# file: diectory/name
# owner: myname
# group: groupname
user::rw-
user:someuser:rwx
group::r--
mask::rwx
other::r--

And use setfacl to set permissions for a user, for example.

# Setfacl, -m = "modify" by adding the user "someuser," giving read, write exec access, to
# directory/name
setfacl -m u:someuser:rwx /directory/name
# And to set it recursively for all subdirectories as well:
setfacl -R -m u:someuser:rwx directory/name

Stanford Cluster Commands

• bsub —– for submitting jobs ```

  General job with input

  bsub -J $JOBNAME -o outfile.{$JOBNAME} -e errfile.{$JOBNAME} ./myscript.sh $INPUT1 $INPUT2

Interactive job

bsub -q IA -Is bash

  - mutt ----- mail client
  - bqueues --- queue information
  - bjobs  ---- show currently running jobs
  - bhist  ---- all job history
  - bpeek  ---- shows recent stdout (for checking on running job)
  - bkill  ---- <*P*>
  - bstop  ---- suspends a job
  - bresume --- resumes the job

## Duke Cluster Commands
  - qsub ----- for submitting jobs

qsub -v $EXPERIMENT=NAME.01 myscript.sh $INPUT1 $INPUT2 ```

• qstat —- job status
• qdel —- delete job

MAC OS

curl -0 http://path.tar.gz

tar -zx # download and unpack

UBUNTU

sshfs name@server.name.com:/path/to/mount /local/machine/folder # use ssh file system to map server on local machine