1. Download the RPM package and install using rpm (not advisable).
2. Download the RPM package and convert to a DEB package using alien
3. Download the ZIP file titled “Oracle SQL Developer for other platforms” and manually install
4. Use the make-sqldeveloper-package to convert the ZIP file into a DEB package

I used the make-sqldeveloper-package, which is available for Debian and Ubuntu and it’s derivatives. However, the man page and the instructions are little unclear on how to use it. You need to download the zip file available at Oracle’s (and not the RPM file nor any of the other packages) and then use the make-sqldeveloper-package to convert it to a DEB which you can then install using the dpkg command.

This is preferable to using rpm or alien as you can more easily manage the package using Debian’s and Ubuntu package management tools, plus it will integrate SQL Developer into Gnome’s Menu System . Plus, when Oracle updates their version you can use make-sqldeveloper-package to create an updated DEB package and easily update the version you have installed. The procedure outlined below works on Ubuntu Karmic and should also work on any Debian version that has the make-sqldeveloper-package.

As the man page states:

This utility will require you to download the “Oracle  SQL  Developer  for  other  platforms”  archive  from  <http://otn.oracle.com/software/prod‐ucts/sql/> to create the Debian package from.

1. Download the ZIP file from Oracle’s site

You will need to accept Oracle’s license agreement and download the ZIP file, titled “Oracle SQL Developer for other platforms”, from:

http://www.oracle.com/technology/software/products/sql/index.html

2. Install the make-sqldeveloper-package package

sudo apt-get install sqldeveloper-package

You will need Ubuntu’s multiverse software repository. See the instructions on how to do so.

2.a. Install the tofrodos package

sudo apt-get install tofrodos

Create symbolic links to the tofrodos commands to allow the sqldeveloper-package to work:

sudo ln -s /usr/bin/fromdos /usr/bin/dos2unix

sudo ln -s /usr/bin/todos /usr/bin/unix2dos

Thanks to Miles for the tofrodos tip.

3. Convert the ZIP file to .DEB package

The format of the command is:

make-sqldeveloper-package -b BUILD_LOCATION LOCATION_OF_ZIP_FILE

In my example, I’m going to use /tmp/ORA as the build location and the ZIP file has been download to my Desktop (~Desktop).

make-sqldeveloper-package -b /tmp/ORA/ ~/Desktop/sqldeveloper-2.1.0.63.73-no-jre.zip

The command will create the build directory and remove it when the command finishes. If the command completes successfully you’ll see the following output after a minute or two:

make-sqldeveloper-package: Building sqldeveloper package in "/tmp".

The DEB file will be created in the current directory. In my example I had changed directories to /tmp and that’s where the DEB file will be:

/tmp/sqldeveloper_2.1.0.63.73+0.2.3-1_all.deb

See the man page for more information about the tool:

man make-sqldeveloper-package

4. Install the package

sudo dpkg -i sqldeveloper_2.1.0.63.73+0.2.3-1_all.deb

5. Run SQL Developer

After installing there should he an entry in Gnome’s menu to start the SQL Developer. It’s located under:

Applications->Programming->SQL Developer

Note: You will need a JVM installed for the tool to run.

Obligatory Screen Shot:

Oracle SQL Developer

Updated September 27th 2010. Added instructions from Miles on installing dos2unix alternative for Ubuntu Lucid. The dos2unix command is not available in Ubuntu Lucid.

Update, Eigensoft 4 is available and should compile on more recent versions of Ubuntu:
http://www.hsph.harvard.edu/faculty/alkes-price/software/

Create a location to build the code:

Warning: /tmp is for temporary files, and any files & directories you create there will be remove upon some subsequent reboot.

cd /tmp;

mkdir EIGEN;

cd  EIGEN;

Get the Eigensoft source code:

wget  http://www.hsph.harvard.edu/faculty/alkes-price/files/EIG3.0.tar.gz;

tar xzvf EIG3.0.tar.gz;

Install required dependences:

sudo apt-get install f2c libg2c0 libatlas-base-dev liblapack-dev;

This symbolic link is needed as the Makefile links looks for the static version of the library and not the shared version (correct me if I’m wrong, it’s late at night and I could be mistaken):

sudo ln -s /usr/lib/libg2c.so.0 /usr/lib/libg2c.so;

Build the code:

cd /tmp/EIGEN;

cd src;

Create a backup copy of the Makefile:

cp Makefile  Makefile.org;

Edit the Makefile:

emacs -nw Makefile;

Change this line (line 24):

FF=g77

To read as:

FF=”gfortran -std-legacy”

This is needed as the g77 fortran compiler is not longer included with Ubuntu, but you can use the gfortan compiler instead, but you must run it in legacy mode.

Run make:

make eigenstrat;

This next step is essential, because binaries are included in the bin directory that appear to have been build against a 64-bit kernel and are probably artefact’s left over from when the author was testing his code. Also, running “make clean” does not remove the binaries in the bin directory, but does remove those build in the src directory.

make install;

And that should be it run the example.perl in the EIGENSTRAT directory and you should see output like this:

./example.perl
smartpca.perl -i example.geno  -a example.snp  -b example.ind  -k 2  -o example.pca  -p example.plot  -e example.eval  -l example.log  -m 5  -t 2  -s 6.0
smartpca -p example.pca.par >example.log
ploteig -i example.pca.evec -c 1:2  -p Case:Control  -x  -y  -o example.plot.xtxt
evec2pca.perl 2 example.pca.evec example.ind example.pca
smarteigenstrat.perl  -i example.geno  -a example.snp  -b example.ind  -p example.pca  -k 1  -o example.chisq  -l example.log
smarteigenstrat -p example.chisq.par >example.loggc.perl example.chisq example.chisq.GC

If you run into problems running and compiling the code, the README suggests running the following:

make pcatoy;

And, as per the README, contact your sys admin if it doesn’t work.

… is a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES (Simplified Molecular Input Line Entry Specification – see http://en.wikipedia.org/wiki/SMILES) or SD file – a computer recognizable molecular structure format. OSRA can read a document in any of the over 90 graphical formats parseable by ImageMagick – including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate the SMILES or SDF representation of the molecular structure images encountered within that document …

Make a directory to compile the source:

mkdir /tmp/OSRA; cd /tmp/OSRA;

Be careful doing this in /tmp is cleaned upon reboot the directory may be removed.

Install dependencies needed by the OS:

sudo apt-get install libgraphicsmagick1-dev libmagick++-dev libgraphicsmagick++1-dev potrace gocr  libtclap-dev libopenbabel-dev libopenbabel3 openbabel libnetpbm10 libnetpbm10-dev

Don’t install ocrad and remove it if it’s on your system (you can probably reinstall if you need to after you get Osra to compile):
sudo apt-get remove –purge ocrad;

Source Code:

Instead of manually getting the source packages download the sources used to build the packages for Ubuntu if available.  Make sure the src lines are commented in, in your /etc/apt/sources.list . This will automatically download and extract the code into the current directory:

cd /tmp/OSRA; apt-get source gocr ocrad potrace;

This downloads Gocr 0.46 which the OSRA docs say may not work:

- GOCR/JOCR, optical character recognition library, version 0.43 or later (version 0.45 recommended, do not use 0.46! See special instructions for 0.47 compilation below)

Get the Osra Source and extract it

cd /tmp/OSRA;

wget http://cactus.nci.nih.gov/osra/osra-1.2.1.tgz;

tar xzvf osra-1.2.1.tgz

cd /tmp/OSRA2/osra-1.2.1;

Make a backup copy of the OSRA Makefile:

cp Makefile Makefile.bak;

Edit the Makefile

Change the following lines:

GOCR=../gocr-0.45/
to
GOCR=../gocr-0.46/

OPENBABEL=/usr/local/
to
OPENBABEL=/usr/

TCLAPINC=-I/usr/local/include/tclap/
to
TCLAPINC=-I/usr/include/tclap/

GOCR=../gocr-0.46/
to
GOCR=../gocr-0.45/

Compiling

Compile, but don’t install the potrace source:
cd /tmp/OSRA/potrace-1.8;
./configure;
make;

Compile the OSRA source:
cd /tmp/OSRA/osra-1.2.1;
make;

This produces a working OSRA binary:

./osra
./osra  [-f <can/smi/sdf>] [-g] [-p] [-s <dimensions, 300x400>] [-n] [-r
<default: auto>] [-o <filename prefix>] [-t <0.2..0.8>] [--]
[--version] [-h] <filename>

Now I just need a file to test it against to see if it will run correctly.

If you want to build with Gocr 0.47 this step is required:
cd /tmp/OSRA/gocr-0.47;
./configure CPPFLAGS=-fPIC LDFLAGS=-fPIC;
make libs;

Python is not Java, tips for Java programmers starting w/ Python:
http://dirtsimple.org/2004/12/python-is-not-java.html
Python for Bioinformatics:
http://www.pasteur.fr/recherche/unites/sis/formation/python/index.html
BioPython:
http://biopython.org/DIST/docs/tutorial/Tutorial.html

I need to know Selenium better, it’s possible that I might consider using it for a project I might be working on (that sounds like it might have some UI bugs/issues/problems):
http://seleniumhq.org/

10 things every programmer should read (this will take a while to wade through):
http://blog.objectmentor.com/articles/2009/02/26/10-papers-every-programmer-should-read-at-least-twice

Xen Cluster Mgt using Ganeti for Debian Lenny:
http://www.howtoforge.com/xen-cluster-management-with-ganeti-on-debian-lenny
Ganeti admin guide and install guide:
http://ganeti-doc.googlecode.com/svn/ganeti-1.2/admin.html
http://ganeti-doc.googlecode.com/svn/ganeti-1.2/install.html

David Byrne (of Talking Heads) interviews Thom Yorke (of Radiohead):
http://www.wired.com/entertainment/music/magazine/16-01/ff_yorke?currentPage=all

With a great quote, that shows how well the record companies treat their performing artists (that’s sarcasm in case you don’t have a sense of humour). First Radiohead made zip/zilch/nada from EMI sales of digitized versions of their music:

Yorke: In terms of digital income, we’ve made more money out of this record than out of all the other Radiohead albums put together, forever — in terms of anything on the Net. And that’s nuts. It’s partly due to the fact that EMI wasn’t giving us any money for digital sales. All the contracts signed in a certain era have none of that stuff …

Yorke: … It’s about whether the music affects you or not. And why would you worry about an artist or a company going after people copying their music if the music itself is not valued?

Then he talks about how the music iteself isn’t valued, but the business processes surrounding the marketing and selling of music:

Byrne: You’re valuing the delivery system as opposed to the relationship and the emotional thing…

Yorke: You’re valuing the company or the interest of the artists rather than the music itself. I don’t know. We’ve always been quite naive. We don’t have any alternative to doing this. It’s the only obvious thing to do.

Now I wonder is there a way to have it only do this for certain types of files, or only to do it for certain workspaces, that way if I’m edit a file in a directory named ruby it will save the files elsewhere, otherwise save the file in the CWD.

apt-get install libstdc++5

Install Aptana:

In Eclipse click on Help->Software Updates. Then click on the Available Software tab, then click on Add Site and paste this URL into the Dialog Box that opens:
http://update.aptana.com/install/3.2/

Eclipse Aptana Install Dialog

Install Aptana, then restart Eclipse. Aptana will then prompt you to install the Subversion plugin, then restart.

When Eclipse restarts following the same procedure as above, except add the following site for Rails support:
http://update.aptana.com/install/rails/3.2/

And restart Eclipse. Aptanta may prompt for further plugins, some of which are from their Professional version which will only work for 60 days.

This works with Eclipse 3.4, and should work on 3.3 and 3.2.

IBM shows how to use RadRails:

http://www.ibm.com/developerworks/opensource/library/os-ecl-radrails/

Complete install instructions:

http://ubuntumagnet.com/2008/01/installing-eclipse-radrails-and-subclipse-under-ubuntu-710-gutsy-gibbon

I was working on test RoR project last night with Emacs, and after a couple of hours imported the project into Netbeans 6.1 (a painless process). When I opened the “.erb” file I had been editing in Emacs, I noticed a panel on the right side of Netbeans titled “Palette”, that allows easy creation of html items such as tables & lists. It also, includes JMaki support for Dojo, Yahoo’s YUI, Scriptaculous, Spry, & JQuery, which allows quick and easy insertion of Ajax features using JMaki. After about 5 minutes of mucking around with various Ajax tables, I was easily able to replace a basic HTML table with a prettier, sortable, Yahoo YUI, Dojo, or JQuery tables.

Here’s a rough example, showing the difference between an list, and a sortable Yahoo YUI table created with Netbeans & JMaki:

This is fairly powerful, and for those inexperienced with Ajax provides a quick and simple way to add Ajax features to a web-page or application as it provides Ruby constructs to create the necessary JavaScript and encapsulates the programmer away from the JavaScript. On the other hand, if your an “ace Ajax guru” this doesn’t allow you to directly write and access JavaScript, and the abstraction might seem like an hindrance.

Here’s a quickie overview showing how to use the JMaki features using a 6.1 beta and Ruby on Rails:

http://blogs.sun.com/arungupta/entry/jmaki_on_rails_reloaded_for

And a more recent generic overview using 6.1 & standard HTML/JSP:

http://www.netbeans.org/kb/docs/web/ajax-jmaki-quickstart.html

What’s also useful, is that JMaki in Netbeans creates the same looking code on your HTML rendering page, which means that if you can create JMaki widgets using Java you can easily do the same with RoR, and presumably with PHP.

If your haven’t looked at Netbeans 6.1 or haven’t tried Netbeans in a while, I do think there are some really useful features that sometime give it the edge over it main competitor Eclipse. I use both IDE’s regularly, and prefer Eclipse for Java & Perl development, but for RoR (especially on Linux) and Ajax features I think Netbeans is the winner (for now). However, there is a JMaki plugin for Eclipse which I haven’t tried that might be comparable (for Java applications).

Using both IDE’s could be a useful addition to a programmer’s toolbox. What I must do next is test Netbeans with a J2EE project created under Eclipse and see if I can use both IDE’s on the same project without problems. It be interesting to see if I can edit the Java code with Eclipse and then modify the view and add JavaScript/Ajax feature with Netbeans.

More information about JMaki can be found at:

https://ajax.dev.java.net/

Updated: Fixed version number, it’s Netbeans 6.5 and not 6.1. Fixed typos from writing tooo fast.

# enable mod_perl
    <Files ~ "\.(pl|cgi)$">
           SetHandler perl-script
           PerlResponseHandler ModPerl::Registry
           Options +ExecCGI
           PerlSendHeader On
    </Files>

In a real production environment you probably don’t want to enable this for all directories that Apache2 serves up, but only from those directories you expect to run perl in.

Thanks to this thread on the Ubuntu Forums for the info.

Titled updated as per Ozkar’s suggestion.

It’s does’t startup as fast as using Emacs, or vi, but I find the features very handy and very convenient. It doesn’t look  bad either. It runs better on my PC at home running Debian Linux than it does on my PC at work running WinXP. This is probably because I’m using a 1.5 JVM on WinXP and a 1.6 JVM on Debian. Running on 1.6 JVM’s means that Netbeans will automatically use anti-aliased fonts if you have anti-aliased fonts enabled (much easier on the eyes if your using a LCD screen).