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.

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

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;

On Debian and Ubuntu you can install the dontzap command which will allow you to kill X:

sudo apt-get install dontzap

Then run dontzap:

sudo dontzap -d

Or you can the following section to your /etc/X11/xorg.conf file (which is what the dontxzap command does):

Section "ServerFlags"
        Option  "DontZap"       "False"
EndSection

See Alberto Milone’s blog for more info:
http://albertomilone.com/wordpress/?p=335

So I think someone needs to look at the math used here, because 3.0.8 is greater than 2.0.0.16. This is using Firefox on Ubuntu Linux.

Update: This may not be a Kayak.com problem and may be a problem with how Ubuntu build Firefox. In the Firefox “about:” page (type about: in the URL bar). It reports the following:

There is a Ubuntu bug that may be related to this, and I’ve added a comment and the screen-shot that’s immediately above.

After lot’s and lot’s of searching I found the ISO images at:
ftp://archive.download.redhat.com/pub/redhat/linux/9/en/iso/i386/

But, there’s too many users on Red Hat’s FTP server and I can’t get access … thankfully rpmfind.net have a mirror:
http://fr.rpmfind.net/linux/redhat/9/en/iso/i386/

So now I can download the ISO images, and mount them on the Linux box using the loop-back interface and install the packages I need.

I expect to have new hardware within a month or so, and I’ll probably be using BU Linux or Ubuntu 8.04.

Ubuntu Jaunty is the new beta version of Ubuntu. It comes with a new version of X.Org and the ATI drivers have been incompatible with this version of X.Org. ATI recently released drivers that support X.Org 1.6. If you have problems with X not starting follow the instructions here:
https://wiki.ubuntu.com/X/Troubleshooting/FglrxInteferesWithRadeonDriver

For me what happened is that X wouldn’t start properly and cause my Lenovo T400 to freeze and lock up. The laptop would boot but when X would start (when the login screen appears) I’d get a black screen with red lines at the top. To solve this I booted to runlevel 1, also known as failsafe mode. If your using a laptop with wireless, I suggest you connect directly to your router using a network cable, otherwise you may have to configure wireless manually (it’s not that hard).

When your system starts, select failsafe mode, on the next screen to appear choose the option to go to a “root shell with networking”.

Next remove the install ATI drivers and install from scratch the ones you need:

sudo apt-get remove –purge xorg-driver-fglrx xserver-xorg-video-ati xserver-xorg-video-radeon
sudo apt-get install xserver-xorg-video-ati
sudo apt-get install –reinstall libgl1-mesa-glx libgl1-mesa-dri
dpkg-reconfigure -phigh xserver-xorg

If this doens’t work for you see the Ubuntu page mentioned above.

The quickest way is to grab a Debian Xen enabled kernel, this isn’t recommended by Ubuntu and if your not comfortable hacking your system and having to compile modules (drivers in Windows speak) for hardware or proprietary hardware that Debian doesn’t include support for, then don’t even think of doing this and just use KVM.

Here’s how Chris did it for a system running a AMD64 processor, if you’ve an Intel processor you’ll need to use a different kernel:

http://www.chrisk.de/blog/2008/12/how-to-run-xen-in-ubuntu-intrepid-without-compiling-a-kernel-by-yourself/

If you want a later kernel (2.6.27 or 2.6.28) poke around:

http://kernel-archive.buildserver.net/

That’s the approach I’m going to use, as I know that if I’ve problems or issues I’ll be able to figure it out. Anyways, the start of the orignal draft is below, preceded by a minor rant. When I get around to getting Xen on Ubuntu to work with a Debian kernel I’ll add a new post here.I recently got a new laptop with a dual-core “Intel(R) Core(TM)2 Duo CPU P8600″ that supports virtualisation. I wanted to retry Xen, and test my new super-duper processors with virtualisation support! I had tried Xen years ago when it was first released, and was pushing it where I worked at the time, but as when I was pushing Linux, people didn’t think it would be viable nor that it would be any good, nor that it could be a competitor to VMWare. I think a lot of this attitude within business is that they don’t really “get” Open Source, and still think that proprietary software processes are always the best.

Within a year of the first big Xen announcement Xen was being pushed and supported by many of the major Linux vendors, but by that time the company had already invested heavily in VMWare and associated tooling and infrastructure and training. Once you do all that, it’s hard to transition to something else, and people become “loyal” to the product their using and resistant to change is high. Don’t get me wrong, VMWare created a great tool, are great people, provide good support (or did last time I talked to them a few years ago), and some have some really smart heads, plus they basically created this “market segment”. But, I’m an Open Source proponent and feel that in many cases Open Source it can save one money, and if an Open Source project is popular and has many interested developers, oftentimes it can be better than it’s equivalent closed-source proprietary brethren. I won’t go into why it’s better in this posting, but a quick Google search will provide you with the pros/cons. Also in my opinion if you use a lot of Open Source you need to hire smart people, who can get things done, instead of hiring drones, and paying someone else a lot of money to do the work for you.

OK, back to the important stuff! I want Xen on Ubuntu Intrepid 8.10, but Ubuntu has discontinued Xen support for versions of Ubuntu after 8.04. They and Red Hat are now moving to a KVM based solution, and Red Hat recently purchased Qumranet; the company that created and supports KVM. Ubuntu still includes the Xen tools with Ubuntu 8.10, which means we only have to compile and install Xen enabled kernels, and simply use Ubuntu package manager to install the tools. If your running Debian Lenny, you can simply use apt-get/aptitude to install Xen kernels and tools. What I aim to do is create Xen kernels, and bundled these as DEB packages which I can then install/remove using Ubuntu’s package management tools.

1. Add yourself to the “src” group:

sudo adduser $USER src

Or replace $USER with the user name of the user you want to have access to kernel source code that is stored in /usr/src . By default kernel source code is stored in /usr/src . If your in the “user” group you can build/compile/modify the code without having to use sudo or “su -”.

2. Install necessary packages to compile, build, and then create a DEB package.

This isn’t a complete list:

sudo apt-get install build-essential libgtk2.0-dev libglib2.0-dev libglade2-dev build-essential libncurses5-dev gawk

3. Get kernel source code.
There are 4 ways to do this:
a. Download kernel source from kernel.org and patch it with Xen patch
b. Download Ubuntu’s kernel source tree and patch it with Xen patch
c. Download Xen’s Kernel source tree that’s already patched with Xen
d. Download Debian’s Kernel source tree that’s already patched with Xen

I’m going with “d”. This will save me from having to patch (and debug) the kernel source tree myself, and then be potentially stuck with unusual bugs, or problems.. This source will have some minimal testing that will at least ensures that it works, and if there are problems I can check Debian’s bug page for their kernel tree.

The easiest way to get the source is to get access to a Debian system and install the source. The source I’m using is 2.6.28, you may end up using a later version:

sudo apt-get install linux-source-2.6.28

This will install the source as /usr/src/linux-source-2.6.28.tar.bz2 . Copy this to your Ubuntu system.

Alternatively download it directly and extract it

Do not install the .deb file on your Ubuntu system as it’s possible that it might overlapse with a future Ubuntu package and cause problems. You can extract the .deb file using the -x flag of the dpkg command:

mkdir /tmp/kernel-src; cd /tmp/kernel-src; dpkg -x <filename>.deb .

Then look in the resultant directory structure for the .bz2 file.

Copy this to /usr/src .

Extract the file:

tar -jxvf linux-source-2.6.28.tar.bz2

Note: If your using pristine Linux sources from kernel.org, don’t extract, until you move or remove the symbolic link named linux.

Rename the resulting directory and bzip file:

mv linux-source-2.6.28 linux-source-2.6.28-debian-xen; mv  linux-source-2.6.28.tar.bz2  linux-source-debian-xen-2.6.28.tar.bz2

I’m using a name that will remind me in the future what I’d used this source code for.

Compile the source code:

To ensure that this works as closely to what Ubuntu uses, I reuse the Ubuntu configuration and enable Xen support. I do this by copying the .config file included with the header files of the kernel version I’m currently running. In this case it’s from a 2.6.27.-13:

cd /usr/src/linux-source-debian-xen-2.6.28;  cp ../linux-headers-2.6.27-13-generic/.config .cd /usr/src/linux-headers-2.6.27-13-generic; fakeroot make-kpkg kernel_image --append-to-version=.custom-xen

Enable 64bit support, enable Xen, enable any additional modules that you want that weren’t in the 2.6.27 kernel and away ye go. The “–append-to-version” is to allow me to ID my kernel, and to prevent any accidental overlaps with future stock  Ubuntu kernels.

If this succeeds, you’ll have a Debian package of the kernel in the parent directory (/usr/src). And that’s where this draft ends and you’ll need to look put the rest of the pieces together yourself! Make sure you have a boot disk, in case grub or lilo get’s borked. And don’t remove your existing kernel until you are sure that your customised kernel works. Best of luck to ye. U can pick up most of the rest of the steps here.

An alternative approach is to install the Debian Packages directly onto Ubuntu:
http://www.chrisk.de/blog/2008/12/how-to-run-xen-in-ubuntu-intrepid-without-compiling-a-kernel-by-yourself/

Useful links:
How to create a custom kernel and package it as a .deb package:
http://newbiedoc.sourceforge.net/system/kernel-pkg.html
How to install a Xen Kernel:
http://www.howtoforge.com/installing-xen-3.3-with-kernel-2.6.27-on-ubuntu-8.10-x86_64
Building DEB packages from Kernel sources:
http://wiki.debian.org/DebianKernelCustomCompilation