ssh tunneling (port forwarding)

The past two places I've worked at have had a single computer that would accept outside ssh communication. However, other computers in the network also had useful things on them but could only be reached from inside the network. How to connect to these other computers directly?

ssh port forwarding allows you to open up an ssh session between you and your gateway computer. Then, you can use that port to interact with the other computers in the network. Here is an example of how to do this:

Open a terminal and type in something like this:

ssh -L<unused_port#>:<final_destination>:22 <gateway_computer>
ssh -L22000:internalserver.super.duper.com:22 gateway.super.duper.com    # e.g.
# you might want to add the -N and -C flags:
ssh -N -C ...
# -N   Do not execute a remote command (useful for forwarding ports)
# -C   compress (for slow network connections only)

Then, open another terminal and you can interact with the internal server as you normally would, just by interacting with your localhost through the specified port:
# log in to the internal server
ssh -p 22000 localhost
# scp stuff from the internal server
scp -P 22000 localhost:~/somefile.txt ./ # copy files from the internal server to local
# mount a folder from the internal server locally using sshfs
sshfs -p 22000 localhost:/home/<user>/<internal_dir> /home/<user>/mnt -o follow_symlinks


Yes that is localhost. You are connecting to port 22000 on the localhost and that is being tunneled via the gateway computer to the internal server!

This works but isn't the absolute slickest setup. Anyone know the equivalent commands for .ssh/config files?

This site has some alternative methods for mounting across ssh.

Fonts in rumai (wmii)

How do you know what fonts you can use in rumai or wmii?
xlsfonts will list all the fonts in the format that wmii expects:

xlsfonts > available_fonts.txt

You can use the '*' symbol to generalize. Here are some that work ok. Some are quite ugly, others OK:

-*-fixed-medium-r-*-*-18-*-*-*-*-*-*-*
-*-fixed-bold-r-*-*-12-*-*-*-*-*-*-*
-*-fixed-medium-r-*-*-12-*-*-*-*-*-*-*
lucidasans-bold-12
-adobe-helvetica-medium-r-*-*-12
-adobe-helvetica-bold-r-*-*-12
-adobe-palatino-bold-r-*-*-14
-*-lucida-bold-r-*-*-12
-*-dejavu sans mono-medium-r-*-*-14
-*-dejavu sans mono-medium-r-*-*-14

wmii (rumai) with gnome in Ubuntu 9.10 & 10.04

NOTE: modified from here

This is a step by step to install rumai as the windows manager in gnome.

1. install necessary packages

sudo apt-get install dwm-tools # for menus
sudo apt-get install libixp libx11-dev  # for the install itself (necessary??)

On Lucid Lynx I needed to install these two packages also:

sudo apt-get install 9base libxft2-dev   # plan 9 file system (need on 10.04)

2. Install a good build
The Ubuntu wmii packages (karmic? and jaunty?) and even the current repo can be buggy. Download a solid build (hg2474) here or here. Unpack it, go into the src directory and sudo make install.
3. modify some gnome settings

gconftool-2 -s /apps/nautilus/preferences/show_desktop --type bool false
gconftool-2 -s /desktop/gnome/background/draw_background --type bool false
## Tell gnome to use wmii as the window manager
gconftool-2 -s /desktop/gnome/session/required_components/windowmanager wmii --type string

4. have wmii fire up at login
System -> Preferences -> Startup Applications Add an entry for /usr/bin/wmii
5. get rumai
make sure you have ruby and rubygems. Works great with ruby 1.9. (I'm using 1.9.1)

gem install rumai

Also make sure your rubygems are executable by adding something like this to your .bashrc:

export PATH="$PATH:$HOME/.gem/ruby/`ruby -e 'print RUBY_VERSION'`/bin"

6. grab a rumai config wmiirc
To make it easy for beginners, my master branch work's out of the box:

git clone git://github.com/jtprince/wmiirc.git ~/.wmii

For more advanced possibilities, you'll want to start with sunaku's and then branch, etc.:

git clone git://github.com/sunaku/wmiirc.git ~/.wmii

Now make a soft link to the file this wmii will be looking in:

ln -s ~/.wmii ~/.wmii-hg

Now logout and back in and it should work. This is pretty stable and works pretty well. If wmii crashes, restart in a terminal or from the panel (add a "run application") with the command "wmii" or "killall wmii && wmii".

multifactorial plotting in R: lattice

I've mentioned before in personal communications that if you have lots of factors in a data set you can just flatten out the data set and then use openoffice data pilot to pivot around different factors (also can be done in ruby with Ruport and 'pivot'). This is a good method.

There is a much better method I recently came across: "trellis plots". The package in R is called lattice.

This is clearly the way to quickly and neatly plot multifactorial data in lots of meaningful ways.

Some resources:

• Excellent Lecture on making trellis plots with lattice (pdf)
• some hype
• The online book on lattice
• code and figures from the book
• ** a table suggesting general forms for each type of plot (thanks Eldon)
  

In R (as sudo if you want system wide installation):

install.packages("lattice", dependencies=TRUE)  # I don't think there are any dependencies
library("lattice")

pymix compilation errors on Ubuntu

pymix was a little tricky to compile. Here's what I did to get it working.

I downloaded and installed numpy [but that is probably not necessary].

Then I finally had to go into pymix's setup.py and change the location for where it was looking for arrayobject.h:
From:
numpypath = prefix + '/lib/python' +pyvs + '/site-packages/numpy/core/include/numpy' # path to arrayobject.h
To:
numpypath = '/usr/share/pyshared/numpy/core/include/numpy' # path to arrayobject.h

At this point, 'python setup.py build' worked, but the install failed with this error:

byte-compiling /usr/local/lib/python2.6/dist-packages/AminoAcidPropertyPrior.py to AminoAcidPropertyPrior.pyc
SyntaxError: ('invalid syntax', ('/usr/local/lib/python2.6/dist-packages/AminoAcidPropertyPrior.py', 170, 14, ' as = alpha.pop(0)\n'))

turns out that 'as' is a reserved keyword in python 2.6, so you need to go in to that file and change it to something else, like: nada = alpha.pop(0)

Bayesian Optimal Discovery Procedure (BODP) R code

The r code given as an additional file to the paper Bayesian optimal discovery procedure for simultaneous significance testing requires your data to be in matrix form. I spent a day trying to troubleshoot the code when all you need to do is the following:

Open R

Copy and paste the R code from Cao et al.

x<-read.table("x.txt") #your control state

y<-read.table("y.txt") #your test state

x<-as.matrix(x)

y<-as.matrix(y)

BODP(x,y,1000,10) #feel free to change 1000 and 10 to whatever you'd like

A thread I started a while ago suggests a solution to getting hibernation and suspend working properly with nvidia cards on Inspiron 5160 in Ubuntu. At least as of Karmic Koala (9.10), the solution one-line easier:

In the device section of /etc/X11/xorg.conf add the line:

Option "NvAGP" "1"

To /etc/modprobe.d/blacklist.conf add the following:

blacklist intel_agp

then reboot

slow browsing in firefox in Ubuntu 9.10 Karmic Koala

type in about:config into the browser bar

change the value of the key "network.dns.disableIPv6" from 'false' to 'true'

drastically increased browsing speed for me.

a little Perl spice for ruby

An insightful blog post got me envying some of the brevity of Perl, so I implemented a couple useful idioms from Test::More in Ruby (which is pretty trivial since it allows opening up a class).

We'd like to have a really terse vocabulary when describing the most common test cases:

## equality
num = 8
num.should.equal 8  # bacon
num.must_equal 8    # minitest::spec
num.should == 8     # rspec
num.is 8            # clearly superior,  similar to Test::More "is a, b"

## true/false
(num == 8).should.be.true # bacon
(num == 8).ok             # superior, like Test::more "ok (something)"

So, for Bacon at least, this is all that needs to be done (put in your spec_helper.rb file)

class Object
  def is(arg)
    should.equal(arg)
  end
  def ok
    should.equal true
  end
end

The argument against this would go, "well, it's better to be more verbose and understood". The counter-argument something like, "this still makes sense and is way easier to write, so I can write more spec's which == better code".

wxruby: wxWidgets for ruby on Ubuntu

A nice link on how to get the basic wxruby (wxWidgets for ruby) going on Ubuntu/debian.

Some examples in the examples folder require some more libraries. For instance, the opengl example requires libopengl-ruby (and maybe freeglut3 libglut [??]) and one of the drawing examples requires librmagick-ruby.

So this should be enough to get you going with most of the examples:

sudo apt-get install libwxbase2.8-{0,dev} libwxgtk2.8-{0,dev} librmagick-ruby libopengl-ruby
sudo gem install wxruby

how to safely delete things in Ubuntu/Linux

I accidentally performed a `rm -rf` on a very big and important directory. I was able to recover close to half of the files using extundelete, but it still left me with a sour taste in my mouth. Now that there is a solid freedesktop specification for how to Trash things, it seems high time to remedy this situation.

In my ~/.bashrc file:

if [ ! `which gvfs-trash 2>/dev/null` ]
then
 alias dl='mv -t ~/.Trash/' # for older systems
else
 alias dl='gvfs-trash'
fi

So, now we can simply dl files and they go to a safe place. Still, I find myself using rm, so this little alias will help cure my addiction, by reminding me that I should be using dl instead of rm. I can still use the rm command by putting it in single quotes (that's how to get past any alias) as in: 'rm' -rf some_directory.

alias rm="echo \"use dl or 'rm'\""

How to share a VirtualBox virtual machine with multiple users on Linux/Ubuntu

Have you ever wanted to share your virtual machine with other users? Doing so will save a lot of space (since you only need one virtual machine) and keep you more in line with the EULA of the distribution you are running virtual (assuming that's Windows or Mac).

There are many tutorials online (for example) that will help you to install VirtualBox on your linux machine. A couple things to note:

1. You probably want to use the package from the VirtualBox download site (and not the open source one that you can get with apt-get) since it has many of the features that are important for a good virtual machine (like USB support and OpenGL acceleration etc).


2. Make sure a vboxusers group was created and that everyone who would want to use the virtual machine is part of that group.

Prerequisite: right now the only way I can get this to work is if everyone wanting to share the virtual machine has sudo privileges. I'd be interested if anyone can suggest a way to do this without them. OK, we're ready to start:

1. Make a shared directory for your virtual machines:

   sudo mkdir /var/local/VirtualBox

2. Create a soft link from the home directory of each user sharing:

   ln -s /var/local/VirtualBox $HOME/.VirtualBox

3. Now create a custom application launcher for your panel:

   sh -c "gksudo 'chown -R $USER:$USER /var/local/VirtualBox'; VirtualBox"

   (that command [or similar] could be wrapped up in a .bashrc function, a script placed in your $HOME/bin directory or whatever).

Also, remember when you buy your next computer to think about getting one with virtualization capabilities (for instance, an intel chart of core 2 duo desktop processors which support virtualization)