What Runs Where on Athena - Utilities

aptitude

Description: Ubuntu command-line package manager
TO RUN:
athena% *aptitude install *package (to install package along with any dependencies)
Many other options exist- see man aptitude for details; the Ubuntu Packages Search page may help with finding packages, their contents and dependencies
*See also: *synaptic
Note: *You will need to sudo to root with {}sudo -i* before running this application to install packages (on public cluster machines, the sudo password is your Athena password). You can do this on debathena-cluster and debathena-workstation or plain Ubuntu machines, but not the Athena dialups. On public machines in Athena clusters, any packages you install will only be installed temporarily, for the duration of your login session

blanche

Description: command-line utility for examining and maintaining Moira lists; such lists can have elements of various types, such as users, lists, strings or Kerberos Principals. Please contact MIT Kerberos Accounts at x3-1325 (Email: accounts@mit.edu) or ***on the Web if you need to have a list set up*
TO RUN:
athena% blanche list -option
Some of the most commonly used options are:
get information about the list:
athena% blanche list -i
show list members of all types:
athena% blanche list -m
add member to the list (if you have permission):
athena% blanche list -a member
delete member from the list (if you have permission):
athena% blanche list -d member
There is also a Web interface (MIT only)
*See also: *lastupd, listmaint, mailmaint, moira, rblanche
There are Stock Answers for creating and editing Athena mailing lists and groups, how do I administer an Athena (Moira) list or group and how to add or delete yourself from Athena mailing lists

brasero

Description: records data on CD-R, CD-R/W and DVD drives
TO RUN:
athena% brasero
Select the type of project you want in the window that opens
*See also: *cdrecord
Note: *Nautilus (the Linux graphical file browser) can burn an iso image file: right-click on the file and select {}Write to Disk*

cdrecord

Description: records data on CD-R, CD-R/W drives
TO RUN:
athena% *cdrecord *file.iso _(to burn an {}iso_ image file)
*See also: *brasero
Note: *Nautilus (the Linux graphical file browser) can burn an iso image file: right-click on the file and select {}Write to Disk*

clean

Description: removes control characters from text files (will convert DOS-style <CR><LF> newlines to UNIX-style <LF>)
TO RUN:
athena% add consult
athena% clean infile outfile
*See also: *dos2unix, unix2dos

CrashPlan

Description: network file backup utility for data on local hard drives; replacing TSM backup for workstation backup
TO RUN:
Install the client locally from here (MIT certificate required) following these instructions

cvs

Description: version control system, operating on hierarchical collections of directories
TO RUN:
athena% cvs options cvs-command _command-options command-args _
see man cvs for more detailed information
*See also: *git, hg (Mercurial), svn (Subversion)

dos2unix, unix2dos

Description: utility that converts text file newline format between UNIX and DOS formats. UNIX normally ends lines with the <LF> character, while DOS ends them with <CR><LF>
To run:
athena% dos2unix file
athena% unix2dos file
The file is converted "in place", replacing the original
*See also: *clean

dosemu

Description: application that emulates a DOS computer. Users have access to a virtual D: drive that mounts their home directory, and a virtual E: drive that mounts a CD or DVD in an optical drive.
To run:
athena% dosemu
*See also: *Mtools
Note: *to access the {}E:* drive you may need to run commands like the following as root before launching dosemu:
mkdir /media/CDROM (if this directory doesn't already exist)
ln -s /media/CDROM /media/cdrom0

dsgrep

Description: allows searching Discuss meetings for text strings
TO RUN:
athena% dsgrep options "-e **{}regexpr*"* meeting
See also: discuss

fs commands

Description: entry point into a large suite of AFS file system commands. These commands will only work if you apply them to a directory that is within an AFS file system. fs help will list available commands. Some of the more commonly used ones are listed below:
TO RUN:
look up access permissions on directory directory:
athena% fs la directory
look up the quota for the AFS volume the current directory is in:
athena% fs lq
set access permission on directory directory for user user:
athena% fs sa directory user acl
where user is a username or AFS group name, and acl is an AFS access control list that contains several letters that set various access permissions. Several shorthand values for acl are allowed: read sets read permission, write sets read and write permission, all sets all permissions and none removes all permissions.
There are Athena and SIPB online documents explaining AFS in more detail; see also AFS at MIT

g3data

Description: utility that captures numeric data values from graphs published in various image formats
TO RUN:
athena% *g3data *options imagefile
There is a Web site
*See also: *fityk_, _OpenRefine, ROOT, Tabula

git

Description: fast, scalable distributed version control system with a rich command set that provides both high-level operations and full access to internals
TO RUN:
athena% *git *[istdraft:options] command [istdraft:arguments]
There are many local git-* man pages- look below* /usr/share/man/man1 to see what these are; see {}man gittutorial* for an introduction; there is much information at the Git home page
See also: cvs , hg (Mercurial), svn (Subversion)

GnuCash

Description: Personal finance manager, similar to Quicken. Used to track income, expenses, investments, etc. There is a GnuCash Web page
TO RUN:
athena% gnucash &

gpg

Description: GNU Privacy Guard, tool for signing and encrypting digital files. Usage is complex and there are many options; the UNIX man page will supply a lot of information; see also the documentation site. There is a gpg Web page
TO RUN:
athena% gpg options file
athena% pgpgpg _options file _(for a wrapper taking pgp command-line options)
athena% gpg -h (for a command summary)
See also: alpine, pgp, pine, ssh

helpquota

Description: Utility that allows users to examine files stored in AFS lockers (including user's home directories), ranked in various ways, and to optionally compress or delete them with the object of staying within the quota on the locker. Files that are generally considered deletable, such as various kinds of backup or temporary files, can be displayed and deleted selectively
TO RUN:
athena% add consult
athena% helpquota options
Note: *Running as {}helpquota -h* will print some usage explanations

hesinfo

Description: Athena-specific interface to portions of the Hesiod database. This database is maintained by Athena Operations staff and contains information about user and filesystem names and ids, groups and various local services as well as resources associated with specific machines. Some typical usage forms are below- see man hesinfo for more
TO RUN:
athena% hesinfo_ name{} filsys (gives file system and local mount point info associated with {}name_(name is an Athena username or locker name)
athena% hesinfo_ name{} passwd (gives password file entry associated with {}name_ (name is an Athena username)
athena% hesinfo_ name{} cluster (gives version information and printers associated with {}name_(name is a computer name)
athena% hesinfo_ uid{} uid (gives username associated with {}uid_ (uid is a UNIX user id number)
See also: lookup

hfs, xhfs

Description: collection of utilities allowing users to read and write to HFS (Macintosh) formatted media. There also are commands that are analogous to equivalent DOS commands with "h" prepended, i.e hdir, hcopy etc.
TO RUN:
athena% hfs (for a TTY command-line interface)
athena% xhfs & (for a GUI interface)
*See also: *Mtools

lastupd

Description: queries moira to determine when servers of a particular type have last been updated
TO RUN:
athena% add consult
athena% *lastupd *servertype
See also: blanche, moira, rblanche

listmaint

Description: text-based menu-driven application for administering Moira lists; types of operation allowed include getting information about lists and their members, adding and deleting members and adding and deleting lists. Many of these operations involve privileges that must be set by Athena administrators. Please contact MIT Kerberos Accounts at x3-1325 (Email: accounts@mit.edu) if you need to get such privileges or have a list set up. There is also a self-service list creation page
TO RUN:
athena% listmaint
There is also a Web interface (MIT only)
*See also: *blanche, mailmaint, moira
There are Stock Answers for creating and editing Athena mailing lists and groups, how do I administer an Athena (Moira) list or group and how to add or delete yourself from Athena mailing lists

lookup

Description: finds AFS volumes(s) a locker is stored on, or volume a user's home directory is on. This is useful when you need to check if a file system is inaccessible due to servers being down
TO RUN:
athena% add consult
athena% lookup locker
athena% lookup username
See also: hesinfo, whichlocker

lsof

Description: lists information about files open for reading or writing on the computer; many options exist- see man page for details
TO RUN:
athena% lsof options
See also: ps

mailmaint

Description: text-based menu-driven application for examining and manipulating Athena mailing lists; emphasis is on operations Athena end-users are allowed to do themselves (add or remove yourself to/from a list, look up lists you are a member of...)
TO RUN:
athena% mailmaint
See also: blanche, listmaint, moira
There are Stock Answers for creating and editing Athena mailing lists and groups, how do I administer an Athena (Moira) list or group and how to add or delete yourself from Athena mailing lists

hg (Mercurial)

Description: lightweight source code management system designed for efficient handling of large distributed objects
TO RUN:
athena% *hg *command _argument options _
See man hg for more detailed information; there is much information at the Mercurial home page and online documentation
See also: cvs , git, svn (Subversion)

moira

Description: general text-based interface to the Moira database. This database contains information about many named entities on Athena, such as usernames, locker names, lists etc. . Access permission is required to view or edit many of the entries
TO RUN:
athena% moira
There is also a Web interface (MIT only)
See also: listmaint, blanche, lastupd, mailmaint, stella, xmoira
There are Stock Answers for creating and editing Athena mailing lists and groups, how do I administer an Athena (Moira) list or group and how to add or delete yourself from Athena mailing lists

Mtools

Description: set of disk file I/O commands similar to DOS ones that allow users on UNIX systems to manipulate files on DOS filesystems (typically on a diskette). ZIP drives are also supported. Wildcarding follows UNIX, not DOS rules
Some of the major available commands:
mattrib - change MSDOS file attribute flags
mbadblocks - tests an MSDOS diskette and marks bad blocks in the FAT
mbackup - script that copies a tree, skipping AFS mountpoints
mcd - change MSDOS directory
mcopy - copy MSDOS files to/from UNIX
mdel - delete an MSDOS file
mdeltree - delete an MSDOS directory tree (use with caution)
mdir - display an MSDOS directory
mformat - add an MSDOS filesystem to a low-level formatted diskette
mkmanifest - creates a script that aids in restoring UNIX filenames clobbered by MSDOS name restrictions
mlabel - make an MSDOS volume label
mmd - make an MSDOS subdirectory
mmount - mounts an MSDOS disk (Linux only)
mmove - moves or renames an existing MSDOS file or directory
mrd - remove an MSDOS subdirectory
mren - rename an existing MSDOS file
mtype - display contents of an MSDOS file
mzip - issues ZIP drive-specific commands
To run:
athena% command file_or_directory
See also: dosemu, hfs

OpenRefine

Description: web-based application for working with messy data, cleaning it, transforming it from one format into another, extending it with web services and linking it to databases like Freebase
TO RUN:
athena% add refine
athena% *refine *
To quit application, type control-C in the launch terminal
There is a home page with links to documentation, tutorials here and here and a Wikipedia article
See also: g3data, R, sas, stata, Tabula

pgp

Description: wrapper that allows pgp command line arguments to be used with gpg
TO RUN:
athena% pgp options file
There is a quickstart guide
See also: gpg, ssh

ps

Description: lists information about processes running on the computer; many options exist- see man page for details
TO RUN:
athena% *ps *options
See also: lsof

rblanche

Description: Recursively lists all members of a mailing list, specifying members of each sublist; also indicates when users have forwarded their mail using chpobox, and if an account is deactivated. Uses the Moira database limited by permissions you have on respective lists
TO RUN:
athena% add consult
athena% rblanche listname
See also: blanche, lastupd

recode

Description: utility that converts files between various character sets and "surfaces"
TO RUN:
athena% *recode *_options [charset | istdraft:request file ] _
Typing info recode and man recode will supply information

renew, grenew

Description: renews user's Kerberos tickets and AFS tokens, which grant access to Athena services and file systems. These are currently set to expire 10 hours after login by default and you will need to renew them if you need to continue the current login session for longer than this. renew *is a command-line utility; {}grenew *runs the same command within a very simple GUI
TO RUN:
athena% grenew &
athena% renew

setup

Description: attaches Athena lockers* and also automatically executes C-shell syntax commands in a file called *.attachrc placed in the top level of the locker (or Bourne-shell syntax commands in .attachrc.bash if you use a Bourne shell or bash)
TO RUN:
athena% setup lockername
Note: *To properly use {}setup*, create a file *.attachrc* or .attachrc.bash and put any initialization commands necessary in it, using syntax appropriate to your shell. These commands will be automatically executed when the setup command is run

svn (Subversion)

Description: version control system offering significant enhancements to older systems like cvs
TO RUN:
athena% svn command options _arguments_
see man svn for more detailed information. There is also a Subversion home page
See also: cvs, git, hg (Mercurial)
Note: *There is also a release in the {}svn* locker, which is older but may have more MIT-specific configuration

synaptic

Description: Ubuntu GUI package manager
TO RUN:
athena% synaptic &
Many options exist, including the ability to add and remove packages, see which packages are installed and view their contents; the Ubuntu Packages Search page may help with finding packages, their contents and dependencies
*See also: *aptitude
Note: *You will need to sudo to root with {}sudo -i* before running this application to install packages (on public cluster machines, the sudo password is your Athena password). You can do this on debathena-cluster and debathena-workstation or plain Ubuntu machines, but not the Athena dialups. On public machines in Athena clusters, any packages you install will only be installed temporarily, for the duration of your login session.
This application is no longer installed. You can install it on debathena-cluster, debathena-workstation or plain Ubuntu machines but not on the Athena dialups by doing the following:
sudo to root and install from the Ubuntu synaptic package by using aptitude

Tabula

Description: utility for extracting data tables from text-based (non-scanned) pdfs
TO RUN:
athena% add tabula
athena% tabula
There is a Web site with usage instructions
See also: Acrobat, fityk, g3data, OpenRefine, ROOT

units

Description: interactive utility that converts various physical quantities between different units of measure
TO RUN:
athena% units

xmoira

Description: utility for managing user's Email forwarding, finger information and default shell
TO RUN:
From Ubuntu Dash: type MIT Account Settings in Search box
From command line:
athena% xmoira
See also: moira

zap-firefox-certs

Description: utility for deleting expired or damaged firefox browser certificates and passwords. Please make sure to exit from any browser instances you are running before using this utility
TO RUN:
athena% *add infoagents *
athena% zap-firefox-certs
See also: firefox
*Note: *You can get a new certificate here

Zip utilities

Description: file compression/decompression programs for single files and directory trees, using the zip compression format. zip and unzip are compatible with pkzip and pkunzip on PCs and create archives of directory trees. gzip and gunzip operate on single files. gzip is often used in conjunction with tar to make compressed archives of directory trees on UNIX systems
TO RUN:
athena% gzip file
athena% gunzip file.gz
athena% bzip2 file
athena% bunzip2 file.bz2
athena% zip archive_name directory/*
athena% unzip archive_name.zip
Note: *bzip2* is a new compression protocol that operates essentially like gzip, but generally achieves higher compression ratios