Admin: Redirected page to Category:Programs

2011-04-08T17:30:59Z

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 All programs listed on this page are free or open-source... unless they have a big dollar sign next to them.
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 [[Category:Computers]]
 [[Category:Programs]]

Admin: /* Unix System Utilities */

2011-04-06T01:25:00Z

Unix System Utilities

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All programs listed on this page are free or open-source... unless they have a big dollar sign next to them.

__TOC__

= My Build Procedure =

When I build programs from source, I use the following setup:

* Programs are all installed in the <code>~/pkg</code> directory

* Tarballs are downloaded to <code>~/pkg/tarballs</code>

* Tarballs are untarred to <code>~/pkg/sources</code> using the command:

<syntaxhighlight lang="bash">
tar xvzf program-x.x.x.tar.gz -C ../sources/
</syntaxhighlight>

* The usual configure/make/make install procedure is performed, but the configure line used is put into a script named <code>runconfigure.program-x.x.x.operating-system.sh</code>, and I put notes into the configure file's comments, so that I have a detailed record of:
** What configure line options I used
** Whether I used a non-standard series of steps, took any extra steps (e.g. <code>make test</code>), or had to install any dependencies
** The date I last modified the configure line

* The program is installed to <code>pkg/program/x.x.x/</code> using the <code>--prefix=$HOME/pkg/program/x.x.x</code> configure option

* (Optional) Once the program is installed, I add <code>pkg/program/x.x.x/bin</code> to my <code>$PATH</code> by adding the following line to my <code>$HOME/.profile</code>:

<syntaxhighlight lang="bash">
export PATH="${PATH}:${HOME}/pkg/program/x.x.x/bin"
</syntaxhighlight>

* Alternately, I can create a link to the "standard version" for my system in <code>$HOME/pkg/program/std</code>, which links to the most up-to-date version of the program; that way, I can install 2 or 3 or more versions of the program, but have the standard version point to the one I want to use. This way, I don't have to update my <code>$HOME/.profile</code> every time, because the <code>.profile</code> contains:

<syntaxhighlight lang="bash">
export PATH="${PATH}:${HOME}/pkg/program/std/bin"
</syntaxhighlight>

= Unix System Utilities =

{|border="1" class="wikitable"
!Unix system utility
!Wikipedia description
|-
|[[Aptitude]]
|
|-
|[[Awk]]
|[[wikipedia:awk]]
|-
|[[Bash]]
|[[wikipedia:bash]]
|-
|[[Emacs]]
|[[wikipedia:emacs]]
|-
|[[Sed]]
|[[wikipedia:sed]]
|-
|[[SSH]]
|[[wikipedia:secure shell]]
|-
|[[Vim]]
|[[wikipedia:vim (text editor)]]
|-
|[[Xargs]]
|[[wikipedia:xargs]]
|}

= Programs Built From Source =

{|border="1" class="wikitable"
!Program
!Link to webpage
|-
|[[Apache]]
|http://httpd.apache.org/

|-
|[[Cantera]]
|http://sourceforge.net/projects/cantera/

|-
|Class library for numbers (cln)
|http://www.ginac.de/CLN/

|-
|[[CMake]]
|http://www.cmake.org/

|-
|[[ctags]]
|http://ctags.sourceforge.net/

|-
|[[Doxygen]]
|http://www.stack.nl/~dimitri/doxygen/

|-
| [[Emacs]]
| http://www.gnu.org/software/emacs/

|-
| [[GDB|GNU debugger (gdb)]]
| http://www.gnu.org/software/gdb/

|-
| [[Ginac]]
| http://www.ginac.de/

|-
| [[googlecl]]
| https://code.google.com/p/googlecl/

|-
| [[gnuplot|gnu plotting program (gnuplot)]]
| http://www.gnuplot.info

|-
| [[gpg|gnu privacy guard (gpg)]]
| http://www.gnupg.org/

|-
| [[HDF5]]
| http://www.hdfgroup.org/HDF5/

|-
| [[Hypre]]
| http://acts.nersc.gov/hypre/

|-
| [[LAM MPI]]
| http://www.lam-mpi.org

|-
| [[OpenMPI]]
| http://www.open-mpi.org/

|-
| [[Petsc]]
| http://www.mcs.anl.gov/petsc/petsc-as/

|-
| [[PHP]]
| http://www.php.net/

|-
| [[Ruby]]
| http://www.ruby-lang.org/en/

|-
|[[Snort]]
|http://www.snort.org/

|-
|[[Subversion]]
|http://subversion.tigris.org/

|-
|[[Sundials]]
|https://computation.llnl.gov/casc/sundials/main.html

|-
|[[Trillinos]]
|http://trilinos.sandia.gov/
|}

= OS-Agnostic (Binary) =

{|border="1" class="wikitable"
!Program
!Description
!Website
|-
|Audacity
|a nice audio recording/editing program
|http://audacity.sourceforge.net/
|-
|[[ffmpeg]]
|all-in-one video processing swiss-army-knife
|http://www.ffmpeg.org/
|-
|[[ffmpeg]]x
|GUI interface for ffmpeg
|http://www.ffmpegx.com/
|-
|[[Fink]]
|Package manager for Mac OS X; makes installing many Unix-based programs much less of a hassle
|http://fink.org
|-
|Gimp
|open-source image editor
|http://www.gimp.org/
|-
|[[Git]]
|a version control system, differs from subversion in a number of ways, designed with a focus on making it easy to branch and merge
|http://git-scm.com/
|-
|Handbrake
|similar to ffmpegx, a GUI interface for converting different video formats
|http://handbrake.fr/
|-
|[[Lapack]]
|Linear algebra package for matrix and vector operations
|http://www.netlib.org/
|-
|[[LyX]]
|a really handy GUI WYSIWYM Latex editor
|http://www.lyx.org/
|-
| [[Matlab]]
| computational package
| http://www.mathworks.com
|-
| Octave
| open-source Matlab alternative
| http://www.gnu.org/software/octave/
|-
| Open Office
| open-source Microsoft Office alternative
| http://www.openoffice.org/
|-
| [[Python]]
| programming language
| http://www.python.org/
|-
|[[Sage]]
|open-source Matlab, Maple, Mathematica alternatives rolled into a Python Swiss Army Knife contained on a VMWare image so it can run cross-platform
|http://www.sagemath.org/
|-
|TexMaker
|Latex text editor
|http://www.xm1math.net/texmaker/
|-
|VLC
|open-source video player that can play just about any video format
|http://www.videolan.org/vlc/
|-
|[[VirtualBox]]
|virtual computer program
|http://www.virtualbox.org/
|-
|Wireshark
|Wireless network traffic analyzer
|http://www.wireshark.org/
|-
|[[x11vnc]]
|a nice VNC program that allows me to set up a remote desktop server (you can then connect to it using your VNC client of choice, I use [[Programs_I_Use#chicken_of_the_vnc|Chicken of the VNC]] on a Mac).
| http://www.karlrunge.com/x11vnc/
|}

= Mac-Only Software =

{|border="1" class="wikitable"
!Program
!Description
!Webpage
|-
|Aquaterm
|version of Emacs that uses Aqua (Mac window style)
|http://aquamacs.org/
|-
|<div id="chicken_of_the_vnc">
Chicken of the VNC
</div>
| remote desktop (or VNC) client for Mac
| http://sourceforge.net/projects/cotvnc/
|-
|Chmox
|utility to read .chm files
|http://chmox.sourceforge.net/
|-
|Disk Inventory X
|gives you a graphical depiction of what's using space on your hard drive
|http://www.derlien.com/
|-
|Divvy
|nice Mac utility to easily resize windows; shareware, but the demo never expires
|http://www.mizage.com/divvy/
|-
|DjView
|utility to read .djvu files (ebook format)
|http://djvu.sourceforge.net/
|-
|[[DynDNS]]
|Syncs IP information with DynDNS servers; allows computers with dynamic IP address to run a web server that DynDNS "knows about"
|http://www.dyndns.com/
|-
|Evernote
|program to take notes, and sync them with a server, on the cloud
|http://www.evernote.com/
|-
|[[Fink]]
|a content-management system (like yum or aptitude) for Mac
|http://www.finkproject.org/
|-
|Fugu
|GUI interface for ftp/ssh/etc to a remote client (Don't use "Son of Fugu", it's not as good as Fugu)
|http://rsug.itd.umich.edu/software/fugu/
|-
|Inkscape
|open-source image editor
|http://inkscape.org/
|-
|iTerm
|alternative to Mac's "Terminal" application (a really nice feature is its full-screen mode: good way to eliminate distractions)
|http://iterm.sourceforge.net/
|-
|[[MacFuse]]
|allows you to mount various file systems on your Mac
|https://code.google.com/p/macfuse/
|-
|[[MacFusion]]
|GUI for using MacFuse to mount different filesystem types
|http://www.macfusionapp.org/
|-
|Mac The Ripper
|used to rip DVDs to your hard drive (extracts to VIDEO_TS and AUDIO_TS, not .mov or .avi, but you can open the VIDEO_TS and AUDIO_TS contents with most DVD players)
|http://www.macupdate.com/info.php/id/14414/mactheripper
|-
|MacPorts
|Don't use Macports, it tries to compile everything, every single last dependency, EVERYTHING, from source (this includes programs that take 5 hours to compile and are already available on your machine and on your path - like gcc). Building anything using MacPorts takes at least 2 hours and MacPorts is a complete waste of time.

I highly recommend Fink. If you're already using MacPorts, I suggest you abandon ship and join Fink... before it's too late.
|
|-
|MacVim
|version of Vim that uses Aqua (Mac window manager)
|https://code.google.com/p/macvim/
|-
|MPlayer
|media player for Mac
|http://www.mplayerhq.hu/design7/news.html
|-
|Shark
|C++ profiler for Mac
|Simple tutorial: http://tuvix.apple.com/tools/sharkoptimize.html

Getting started: http://bit.ly/a4XYEv

Advanced profiling: http://bit.ly/9ffZd7
|-
|Saturn
|another profiler for Mac
| http://adrianboeing.blogspot.com/2010/02/profiling-on-mac-osx-with-saturn.html
|}

[[Category:Computers]]
[[Category:Programs]]

Programs I Use - Revision history

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Admin: /* Unix System Utilities */