haotu : an open lab notebook


Text Editors for Python

Filed under: Python, Ubuntu, Windows 7 — S @ 11:28

1. I installed IDLE for python and am using that as a text editor. However I found this blog:


And PyDev looks good http://pydev.org/ so I might try that especially since I might be able to use it in Windows 7.

2. I had to install Eclipse in the software center, however, the version was old, so I dled eclipse calssic as a tarball from the eclipse website.

3. In order to install eclipse I followed the manual instructions on this wiki https://help.ubuntu.com/community/EclipseIDE#User%20installation

User installation

Use this method if you want Eclipse available only for yourself, or if you do not have root access to the computer. It is also useful for those who would like to install newer versions of Eclipse (eg. Eclipse 3.3 or Eclipse 3.4).

Download Eclipse

Open a web browser and go to http://www.eclipse.org/downloads/. There are several different bundles of Eclipse geared toward the different types of software development. You could take a basic Eclipse installation and manually build it into any one of these bundles. They are provided pre-bundled as a convenience for the developer. When in doubt, download the “Eclipse Classic” bundle. It is the most traditional bundle of Eclipse on the list. Select the Linux 32bit package, or 64bit if you’re on an x86_64 system.

Preparing your system

We will set up a few folders for Eclipse in your home directory and unpack the Eclipse package into those folders.

Make an opt folder in your home directory:

$ mkdir ~/opt

Change directory to the folder where your browser downloaded the Eclipse package to. Then unpack Eclipse into the opt folder:

$ cd {directory where your browser downloaded the package to}
$ tar -xvf eclipse-SDK-3.4.1-linux-gtk.tar.gz && mv eclipse ~/opt

Make a bin folder in your home directory, this will be used for the startup script:

$ mkdir ~/bin

Next create an executable for Eclipe at ~/bin/eclipse with your favorite text editor by typing vi ~/bin/eclipse or nano ~/bin/eclipse into the command line. Add the following content:

export MOZILLA_FIVE_HOME="/usr/lib/mozilla/"
export ECLIPSE_HOME="$HOME/opt/eclipse"

$ECLIPSE_HOME/eclipse $*

Finally, allow the script to be executed:

$ chmod +x ~/bin/eclipse

HINT: If you are a gtk user and experience problems with the mouse buttons you should try add an export:


to the starter file.

You can now execute that file to start up Eclipse.

Gnome icon

Create a new launcher on the desktop (right click on the desktop -> Create Launcher) or on a panel (right click on a panel -> Add to Panel -> Custom Application Launcher)

  • Name: Eclipse Platform
  • Command: /home/<your username>/opt/eclipse/eclipse
  • Icon: /home/<your username>/opt/eclipse/icon.xpm

4.Then to setup PyDev I followed the instructions on the PyDev manual page


These instructions unfortunately did not work I think because I did not install eclipse correctly…

Change Boot Order Ubuntu Grub

Filed under: Lynux, Ubuntu — S @ 07:12

The default for Ubuntu after I installed it as the last post was to have Ubuntu first and the Windows OS systems last in the boot list. I installed the startup-manager through the ubuntu software center and used it to set my Windows 7 OS as default. I was also able to change the timeout setting so that I had more time at the bootup to choose which OS I wanted to run.


Install Ubuntu on a hard drive partition on a Windows 7 Sony VPCEB

Filed under: Lynux, Ubuntu — S @ 13:40

Below I will outline the steps I took to figure out how to install Ubuntu on my Sony EB series laptop. I have installed Ubuntu on a partition on a Lenovo Windows 7 machine before… so I hope this time it will be easier.

1. I am starting here: https://help.ubuntu.com/community/WindowsDualBoot

2. Install Ubuntu

3. There is a Windows installer here too. I decided not to use it since it was a slightly older version of Ubuntu and it was not clear if I could make a drive partition in the process.

4. I downloaded the 64 bit .iso

5. I downloaded and installed infra recorder as what is said in the Ubuntu instructions: http://infrarecorder.org/. I could have also just used Windows 7 right click and it works.

6. I burned the disk image

7. Then i rebooted the computer with the CD in the drive and followed the instructions. I choose to Install them side by side, choosing between them each startup since that is what the instructions said to do and it was easy.

8. My trackpad however did not work, thus I went to this forum http://ubuntuforums.org/showthread.php?p=10533193

enter command

sudo nano /etc/default/grub

Change the line




then issue the command

sudo update-grub

and reboot.

9. It seems to be running fine. I ran the Python script that was given to me by Stefano Allesina to obtain taxonomy trees.

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