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).
A user at work reported that ChemDraw suddenly started segfault-ing (crashing) on startup on his Mac. He’d opened a support ticket with CambridgeSoft and tried their suggestions, basically deleting every file associated with ChemDraw and reinstalling, which didn’t correct the problem.
I suspected that this was an issue with ChemDraw 12.0.2 (I’m using 12.0.1 and so are other CMLD members for the research lab I support). I suggested that he create a new user on his Mac and see if ChemDraw works correctly. I reasoned that ChemDraw was upgraded sometime in the past, and that there may have been some user preferences causing issues after upgrading, or some preferences settings were corrupted.
If a new user was able to use ChemDraw, then this would indicate that the installation is valid and working, and the issue is with the user’s preferences. If ChemDraw didn’t work, then the issue is probably with the installation, and we would need to install the application, and hunt down any remnants of the installation that may be in /Library or /System and then reinstall 12.0.1 to see if that would resolve the problem.
In this case, ChemDraw worked for the new user, thus indicating that the issue was not with the installation, but with the user’s setting. Deleting any files whose name started with com.cambridgesoft files in
Friday before I left work I kicked off the upgrade to Mac OS 10.6.3 on the MacBook Pro (MBP) I use at work. I’d already upgrade my personal MacBook at home (that I got a deal on at MicroCenter) and I didn’t have any observeable problems or issues and I was confident that I could upgrade and not bork my work environment.
When I arrived back into work on Monday it looked like the upgrade had completed. I logged into the MBP and my Bluetooth MagicMouse wasn’t working, and all bluetooth settings were unavailable and grayed out (both on the status bar, and in System Preferences).
I figured something had gotten out of sync during the upgrade and I thought a reboot would fix the problem. Rebooting didn’t fix the problem, but manually reinstalling the upgrade did solve the problem and Bluetooth is active and settings are accessible.
Recently I updated the wp-supercache plugin. It’s a plugin for WordPress which is the blogging software that runs this site. Wp-supercache is used to cache pages and is very useful if this blog should happen to get Slashdotted.
Wp-supercache now supports the wp-mobile plugin. What isn’t obvious from the wp-supercache settings is that you need to install the wp-mobile plugin. Get it at http://wordpress.org/extend/plugins/wordpress-mobile-edition/ unzip it, and then read the included README.txt to configure it properly.
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.
Just back from a trip home to Ireland and am pooped. Got up at 6am (1am EST) and drove up to Dublin Airport from Donegal Town via Omagh. Got there about 10.30am, would have been earlier but the car was running on fumes and I had to stop for petrol. As I was whizzing down the M1, my cousin John, whom I gave a lift to the airport, said there’s no services on that motorway. Which lead us on a 30 minute detour trying to find some petrol pumps in the wastes of Louth! 😉
Got to the airport at 10.30am, dropped off the car, had a ciggie, met my friend Eamon L. who dropped out to see me off and had a nice big (expensive) breakfast before going through security. Had 3 jumbo sausages, 2 rashers, 2 slices of thick toast, 1 egg, 1 hash brown, 1/2 a fried tomato, and numerous backed beans.:) A good end to a long drive, and a nice fill-up before a long flight.
On the plane I got 2 seats to meself and dosed off for about 2 hours or more after they served “dinner”. Woke up somewhere over the Canadian north and got to watch the lame ending to the last Harry Blouter film.
At Logan (Boston’s airport), I got through everything quickly, and didn’t have to wait too long for a shuttle bus to the blue line on the subway. And it wasn’t too busy considering it was rush hour. I guess most of the commuters were heading the other way. I changed Gov Center for the Green Line that goes near the house, and lucky enough I got a local train going to Kenmore (never seen one of those before) which was nice and quiet and not full of rush-hour nasties. And got home in time to see the sunset.
So now I’m pooped, as it’s 11:45pm Irish Time, and I need dinner … pics will appear on Flickr at some point.
Update: Here’s one! 🙂 More via this Flickr search.
