PRIME - Linux workstations and servers - Installed Software

The following notes describe software and features on the Prime ring of Linux servers and workstations that can be accessed by individual users. This is not an exhaustive list, as the standard Unix tools and commands are also available. If you are not sure what you are looking for, try a keyword search on the manual pages with the command:

man -k KEYWORD
Or try google for more information.

Software Categories

META control packages
Editors, Text Processors, word processors
Compilers, interpreters and extensions.
Source code checkers and debuggers.
General libraries, located in /usr/local/lib unless noted:
Software development packages
Web browsers and file downloaders/uploaders
MAIL PROGRAMS
Graphics/picture utilities
Graphics libraries
Data bases
Software Version Control Systems
Archiving Systems
Networking tools - you need root to actively sniff all packets, but you can see your own!
Compression/decompression utilities
Computational libraries
Games

META control packages

VirtualBox - virutal machine software (linux machines only.) Get the user manual from THIS PAGE
Get virtural machine images for various operating systems from:
virtualboximages.com
virtualboxes.org.
SHELLS
Shells available include:
bash
sh - just linked to bash, so it is not 100% compatable with the borne shell
csh
ksh
zsh
tcsh

Editors

vim (vi) - visual editor - cheat sheet at http://www.lagmonster.org/docs/vi.htmla
ex - line mode interface to vi - useful if full screen editing is not avaliable
ed - Old line mode editor
sed - batch mode editor using vi/ex commands to edit a file
nano - Simplified replacement for pico, vi, vim (new version of vi)
pico - replaced by nano, but you can use pico as the command name.
emacs - not just an editor but a way of life
atom - hackable editor - see https://flight-manual.atom.io/getting-started/sections/atom-basics/

Word Processing, document generation, etc

libreoffice tex (texlive) - both tex and latex are available with support programs
doxygen - documentation system for C++, C, Java, Objective-C, IDL, etc
cxref cxref-doc generate LaTeX and HTML docs for C programmers
groff, nroff, troff, ... typesetting system for documentation
spell - spell checker
ghostscript - gv - view postscript file
graphviz - graph visualization software. on-line documentation.

Compilers and Interpreters

GNU C and C++
Fortran - fort77 , gfortran
Go
Lisp is available as gnu common lisp, clisp and gcl
Prolog - GNU prolog incoudes pgrolog, gplc, etc
Python - python3 and python2.7, and pip
R
Ruby - ruby
Scheme - MIT/GNU scheme
clang
erlang
llvm
ocaml
perl

Extentions to compilers

Boost extensions for C++
libmpfrc++ - multi-precision floating point number class for C++
gccxml - parses a C++ source file as it is seen by the compiler when it is built
castxml - replacement for gccxml
rapidjson - a JSON parser and generator for C++

Source code checkers

cscope - allows the user to browse through C source files for specified elements of code
cflow - analyzes a collection of C source files and prints a graph, charting control flow within the program
cppcheck - Command-line tool that tries to detect bugs in souce code that gcc does not see.
spin Formal verification of software systems.

Debuggers

gdb - gnu debugger - Manuals or an interactive web based version at sourceware.org
ddd - visual debugger using gdb
valgrind - debugging and profiling programs
valkyrie - visual front end to valgrind
kcachegrind - is a visualisation tool for the profiling data generated by calltree, a profiling skin for valgrind
gcov - test coverage program
ggcov - gui interface to gcov
lcov - gui interface to gcov
sleuthkit - analyze hard drives and smart phones - www.sleuthkit.org
autopsy - digital forensics platform and graphical interface to The Sleuth Kit
mac-robber - a digital investigation tool that collects data from allocated files in a mounted file system

Software development packages

Visual Studio is a source code editor with built-in support for JavaScript, TypeScript and Node.js and extensions for other languages (such as C++, C#, Java, Python, PHP, Go) and runtimes (such as .NET and Unity).
Eclipse Java development platform.
ispin - graphical interface to spin.
Netbeans - IDE for JavaScript, HTML5, PHP, etc development
Maven a software project management and comprehension tool.
cmake a cross platform, open-source build system.

General libraries

openmpi- A High Performance Message Passing Library Docmentatation list
libjansson - C library for encoding, decoding and manipulating JSON data

Command Line Web Browsers and File Transfer Programs

curl is a command line tool for transferring files with URL syntax, supporting FTP, FTPS, HTTP, HTTPS, SCP, SFTP, TFTP, TELNET, DICT, LDAP, LDAPS and FILE. curl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, kerberos...), file transfer resume, proxy tunneling and more.
lynx - web browser for terminals and batch processing
links - Updated version of lynx web browser for terminals and batch processing
elinks - another text based web browser. Online documentation is here.
wget is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals etc, for retrieving files using HTTP, HTTPS and FTP.
urlview - Extract URLs from a text file and allow the user to select via a menu
lftp - a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent)
tftp - Trivial File Transfer Protocol
wput - - command-line ftp-client that looks like wget but instead of downloading, uploads files or whole directories to remote ftp-servers

GUI Web Browsers

firefox - web browser
chromium - web browser

MAIL PROGRAMS

evolution - GUI email reader
mutt is a small but very powerful text-based mail client for Unix operating systems.
alpine a fast, easy to use email client that is suitable for both the inexperienced email user as well as for the most demanding of power users (or so they say). It is the successor to pine.
Alpine
mailx - A unix mail reader/sender, system V version.
vacation - returns a message to the sender of a message telling them that you are currently not reading your mail1
Web mail via any web browser

Graphics/picture utilities

The Gimp - photomanipulation like photoshop.
Tcl/Tk Tk is a graphical user interface toolkit
ImageMagick - create, edit, compose, or convert bitmap images. in over 200 formats, command line or via library calls.
GraphicsMagick - A fork from Imagemagick
dia A diagram creation tool that supports UML modeling.
xclip - command line interface to X selections (clipboard)
plotutils - use the info plotutils command for more information
xplot - plot one- or twodimensional datasets,
gnuplot - command-driven interactive plotting program, using multiple files or functions

Graphics libraries

mesa-utils - for Open-GL programming
libglfw3 - is an Open Source, multi-platform library for OpenGL.
libglm - OepnG Mathematics (GML) is a header only c++ math library or graphics software based on the OpenGL Shading Language (GLSL) specifications.
jbigkit - library and toosl for JBIG1 data - bi-level images
libgif - library and tools for GIF files
libpng is a free reference library for reading and writing PNGs (Portable Network Graphics)
libtiff - library and tools for tiff files
libjpeg - library and tools for jpeg files
libxpm - library and tools for xpm files
libgts - library and tools for 3D computational surface meshes
ncurses library
libsdl - Simple DirectMedia Layer is a cross-platform development library designed to provide low level access to audio, keyboard, mouse, joystick, and graphics hardware via OpenGL and Direct3D.

Data bases

sqlite - mini verison of mysql Documentation.

Software Version Control Systems

CVS is a version control system. Using it, you can record the history of your source files.
SVN an open source version control system that superceeds and is is very similar to CVS,
git a "faster" version control system, with a large amount of on-line documentation.
Mercurial a fast, lightweight Source Control Management system designed for efficient handling of very large distributed projects.
bazaar - bzr distributed and client-server revision control system sponsored by Canonical
rpm2cpio - convert rpm file to cpio format, allowing easy extraction of files

Archiving system

gtar (gnu tar) provides the ability to create tar archives, as well as various other kinds of manipulation.
gzip a popular data compression program, which includes the programs:

Networking tools

wireshark THE network protocol analyzer, developed by an international team of experts.
tshark terminal mode version of wireshark - Xwindows not required.
tcpdump - dump traffic on a network
tcptrace - gives stats on tcp connections
libpcap The Packet Capture library provides a high level interface to packet capture systems. All packets on the network, even those destined for other hosts, are accessible through this mechanism.
nmap - Network MAPper - utility for network exploration or security auditing. In addition to the classic command-line Nmap executable, the Nmap suite includes an advanced GUI and results viewer (Zenmap), a flexible data transfer, redirection, and debugging tool (Ncat), and a utility for comparing scan results (Ndiff).
traceroute, ping, pign6, netstat, etc.

Compression programs

compress (actually, ncompress)
zip (and unzip)
gzip ( and gunzip) - the GNU version of zip.
bzip2 ( and bunzip2) - A public domain compression routine, with some additional features, such as the ability to sometimes recover compressed files that are damaged.
rar unrar
p7zip p7zip-full p7zip-rar
snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.

Compression libraries

zlib compression library.
bzip library
snappy library

Computational libraries

bmplib -the GNU Multiple Precision Arithmetic Library.
GSL - GNU Scientific Library
MPFR library is a C library for multiple-precision floating-point computations with correct rounding.

Games

neverball - Tilt the floor to roll a ball through an obstacle course before time runs out.
neverputt - Original minigolf from the makers Neverball
nethack-x11 - a single-player roguelike video game originally released in 1987 with ASCII graphics
nethack-console - a single-player roguelike video game originally released in 1987 with ASCII graphics