Installing LibSBML on Ubuntu
- first, install all the necessary packages:
aptitude install build-essential libxml2 libxml2-dev python-dev
- then configure, make and install libsbml:
./configure ––with-python (execute from the directory where the downloaded libsbml archive was extracted to)
make
make install
ldconfig
- then check if installation was successful:
python
and when the python prompt >>> appears, run from libsbml import * – if there are no warnings/errors, then you are done!
Installing MoinMoin 1.9 on Ubuntu
This series about MoinMoin is something that is long overdue. Everything you need to know about installing and configuring MoinMoin (from here on we call it MM) is well documented at the above link and also on numerous blogs. Why do I write this article then? The following will distinguish my articles on MM with others on the net.
- The workflow described here is optimised towards backup and security
- This workflow reduces administration tasks during future server migrations
Note that these articles explain the workflow I follow. There are of course many other ways to approach the same problem. Please do let me know if you have a better method.
Software Required
MoinMoin Version
At the time of writing this, the latest stable version of MM is 1.9.3. However, you can adopt the methods described here on previous versions as well. If you are new to MM, there is less chance of you noticing any differences between the recent versions.
Platforms
I have been using this appoach on Ubuntu 8.04 LTS (Hardy Heron) onwards. Currently, I have Ubuntu 10.04 LTS (Lucid Lynx).
Requirements
Have a look at this link on MM website to have a list of dependencies for different versions.
Articles in this series will be describing MoinMoin 1.9.3 on Ubuntu 10.04 LTS. However, I would like to reiterate the point that you can use it on other combinations as well.
Installation
The actual installation of MM on Ubuntu is as simple as typing the following code:
sudo apt-get install python2.4-moinmoin
This will install MM at /usr/share/moin/ and the config files will be stored at /etc/moin/. The issue with installing at this location is that most of us dont normally backup /usr/share/. Personally, I prefer to keep all such important applications under /usr/local/applications/ directory. I take particular care to make regular backup of my /usr/local/ directory. This way the only thing I have to do in case of a server crash of some sort is to restore this directory. So, how do we install MM to /usr/local/applications?
- Download MM from here
- Extract using tar as follows
tar xvzf moin-x.x.x.tar.gz - Navigate to the directory where you extracted MM
- Install MM using:
python setup.py install --force --record=install.log --prefix='/usr/local/applications' --install-data='/usr/local/www/template
where:
–force = To overwrite outdated files in the destination (not needed in this case).
–record = This is the install log. Keep this safe, just in case.
–prefix = Our installation location. This is where our MM installation is now located.
–install-data = This where we are going to keep our MoinMoin instance. Read my second post in this series to see what we do with this directory.
Great! we have MoinMoin installed on our server. In my next post I will explain how to get our first wiki on the internet. All the above information is explained in much more detail in the MM website and also on the install.html file that comes with the MM download. But then, you wont be reading this if you have read those documents!
A Fast And Non-resource Hungry Backup Stategy For Ubuntu
I love command line, and I spend most of the day working with a black-and-white terminal. For this reason, ever since I started with Ubuntu, I have been using rsync and cron for backing up my files (in one of my previous posts, I have provided a detailed how-to on backing up subversion repositories using rsync). However, not so long ago, I came across a very useful GUI for rsync and cron based backup called ‘luckyBackup’. I liked this software as it allowed me to visualise all my backup cron jobs in a single window. For some reason the experience of using this tool was a bit more reassuring than what I used to do. Some of its features such as multiple profiles, exclude/include files/directories, synchronisation etc were found to be very handy.
Now that I have started working with RAW and DNG photographs, my workflow demands an efficient backup solution. I work on these files using Adobe Lighroom and Photoshop (I prefer them more than Gimp) on a VirtualBox WindowsXP. I have configured luckyBackup on my server to make backup of my RAW files every 12 hours to two independent locations – an internal backup only hard drive and a portable hard drive. luckyBackup emails me when the target directories are 25GB in size, so that I can then write it on to a Blue-Ray disk and lock it up safely.
The old church of Marten
This is one of my very first High Dynamic Range (HDR) images. I am really proud of this photo. However, I feel that the pole at the center is a big deterrent. I think I will have to work a lot on my Photoshop skills to get it wiped off. Well, I tried the smart select and delete option. Any other ideas are welcome.
Nondestructive Photography Workflow That I Follow
Following flowchart illustrate the nondestructive workflow that I keep up to manage and edit my photographs. I hope that the illustration is self explanatory. The software Adobe DNG (Digital Negative) mentioned in the illustration can be downloaded for free from http://www.adobe.com/products/dng/.
The color profile of the camera is set to AdobeRGB. All RAW editing is done with software that are set to work in this color profile. My camera (Canon EOS450D) produces 14-bit RAW images (Only a few very high-end cameras actually record more than 12 bits of data in the 16 bits that are available to RAW files). The 14-bit RAW can, if needed, be converted to 16-bit using the software that comes with the camera. RAW files are nondestructive – the only way one can destruct it by deleting it from the system. Which means that any change done on the RAW files can be undone if and when necessary. I tend to save all the processed images as TIFF files (8bit). All photograph winnowing is done using Adobe Bridge.
Something I Always Wanted To Do
I used to do a lot of oil and water color painting years ago. Ever since I bought my first computer, I drifted away from any kind of art work. Then one day I came across flickr and was amazed by some of the photos on display. But very soon I realised how expensive a hobby that is. Nevertheless, after many years of counting coins I bought a DSLR, but then couldn’t find enough time to any serious photography. Now I am desperately in need of a new hobby to get away from the many intricate matters that bog my mind. I decided to go back to photography and here are some of the photos that I made recently.
Merging a Subversion Branch With Trunk
A most confusing thing to do in subversion is to merge a branch with a trunk. One might need this in cases where the branch has grown and has to be made a trunk. Following is a step by step how-to on doing this the proper way.
1. Check out the trunk or update an earlier working copy of the trunk
svn co file:///repository/project/trunk project2. Merge the branch with the working copy
svn co file:///repository/project/trunkfile:///repository/project/branches/branch project
The arguments are -
a) An initial repository tree (left side of comparison)
b) A final repository tree (right side of comparison)
c) A working copy to accept the differences as local changes
This means that you can also give version numbers, for example:
svn co file:///repository/project/trunk@100 file:///repository/project/branches/branch@114 project3. Now that the merging is done, go into the working copy and commit the changes.
svn commit -m "merged branch@114 to trunk@100"Merging is very important and of frequent use during version control.
Installing Fonts in Ubuntu
Copy your fonts into the .fonts directory in the home directory and then update the font cache with this command:
sudo fc-cache -fv
To use it with LaTeX fontspec package (it can use open-type fonts directly in your document), you will need is to take note of the exact name of the font family. For that, after having installed the lcdf-typetools Ubuntu package, you can do something like
otfinfo -i /usr/share/fonts/AGaramondPro-Regular.otf | grep Family
SSHMenu – A Really Cool Gnome Addon
Checkout out this great tool for Gnome at http://sshmenu.sourceforge.net. This tool, in combination with ssh-copy-id, can help you switch between your ssh servers in one click. Type the following to try SSHMenu:
sudo apt-get install sshmenu-gnome
Note that you have to add it to the gnome panel to use it.
Removing .svn Directories From Subversion Checkouts
Use the following command to remove .svn directories from unwanted subversion checkouts.
find -iname “.svn” | xargs rm -r $1
Alternatively, you can commit all recent changes and use svn export to get the current version without .svn directories.
