Osra is a a utility designed to convert graphical representations of chemical structures create by Igor Filippov at the National Cancer Institute. This page documents how to compile and install Osra on Ubuntu Linux 11.10. These instructions may work on other versions of Ubuntu Linux and on Debian Linux. Please leave a comment if you have compiled Osra using these instructions on a different version of Ubuntu, or on other Linux distributions.
Overview
At the time of writing this doc, March 2012, the Osra version is 1.3.8 and is available at:
I copied all the source to a directory in /tmp. If you need the source code at some later point in time, don’t use /tmp as files in /tmp are deleted upon reboot (if they’re older than 14 days). Also, at the time of writing Osra requires a patched version of Gocr for Osra to work. You need to install Gocr before you try to compile and install Osra, you also need to install other packages required for Osra to compile. Most are listed below, but see the Osra Homepage for more details.
This is a fix for the bug where Cogs launches with the following output:
Shader compile log for data/effects/TextureBumpCubemap.fsh:
Fragment shader failed to compile with the following errors:
ERROR: 0:41: error(#132) Syntax error: ‘smooth’ parse error
ERROR: error(#273) 1 compilation errors. No code generated
Apparently the word “smooth” is reserved, but only on ATI cards in Linux. The fix is to modify the following file.
~/games/cogs/data/effects/TextureBumpCubemap.fsh
Just do a global replace of the word “smooth” with “Smooth”.
A huge thanks to Renee Marie Jones, who figured this one out
I wasn’t seeing that particular output on the console, and the screen was just blank/black and I could hear the music. But, this fix did work for me on Ubuntu Linux 10.10 (Maverick).
If you want to install Oracle’s SQL Developer on Ubuntu (or another DEB based system such as Debian) you can do one of the following:
Download the RPM package and install using rpm (not advisable).
Download the RPM package and convert to a DEB package using alien
Download the ZIP file titled “Oracle SQL Developer for other platforms” and manually install
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:
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:
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.
This is a brief HOWTO on compiling OSRA, (Optical Structure Recognition) on Ubuntu Jaunty. To quote the OSRA home page, OSRA is
… 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 …
Update: I’ve a newer document that shows how to install Osra on Ubuntu 11.10 (Oneiric):
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) Continue reading Compiling Osra on Ubuntu Jaunty→
On Ubuntu it used to be that ctrl-alt-backspace would kill X (the backend of the various graphical user interfaces on Linux). In an aim to be user friendly this is now disabled by default. This can be a real pain if X locks up, you can’t kill it nor change to a console.
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):
I use Kayak.com whenever I’m planning a trip any where, it’s a good source to determine who flies to what destination and whose got the lowest price. Today, there’s a wee bug on their website where they tell me I should upgrade to Firefox 2.0.0.16, this would be sound advise except for the fact that I’m using a newer version of Firefox:
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.
I have a Red Hat 9 server that I have to support for a wee while longer. I needed to install some packages and I didn’t have the original install CD’s nor access to Red Hat’s repositories.
