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:

• http://cactus.nci.nih.gov/osra/#6

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.

An overview of the steps are:

1. Install required Ubuntu packages
2. Compile and Install Gocr
3. Compile and Install Osra

I’ve also written instructions on how to install Osra 1.2.1 on Ubuntu 9.04, however that was written in 2009.

Install Ubuntu Packages

These packages are required to build Osta. Install the following (you will also need some gaphicsmagick packages also, libgraphicsmagick1-dev libgraphicsmagick++3 and maybe some others).

sudo apt-get install libtclap-dev libpotrace0  libpotrace-dev  libocrad-dev openbabel libopenbabel-dev  libgraphicsmagick++1-dev libgraphicsmagick++1-dev libgraphicsmagick++3 libgraphicsmagick1-dev libgraphicsmagick3 libnetpbm10-dev

Quick Install

Copy and paste the following line to make a directory in /tmp called OSRA, download the source, extract the packages, and build and install both:

cd /tmp; mkdir OSRA; cd OSRA; wget http://cactus.nci.nih.gov/osra/osra-1.3.8.tgz ; wget http://cactus.nci.nih.gov/osra/gocr-0.50pre-patched.tgz ; tar xzvf osra-1.3.8.tgz; tar xzvf gocr-0.50pre-patched.tgz; cd /tmp/OSRA/gocr-0.50pre-patched; ./configure; make libs; sudo make all install; cd /tmp/OSRA/osra-1.3.8/; ./configure; make all; sudo make install

Osra should be  installed in /usr/local/bin .

Below are the same steps, but with more detail so that you know what your doing:

Create Directory to Build the Packages

mkdir /tmp/OSRA

Download the Source

If you have wget install you can download the source via the command line:

cd /tmp/OSRA;

wget http://cactus.nci.nih.gov/osra/osra-1.3.8.tgz ;

wget http://cactus.nci.nih.gov/osra/gocr-0.50pre-patched.tgz

Otherwise go to the Osar home page and download the source code pacakge for both Osra and Gocr and save it in the directory you created.

Extract both packages

tar xzvf osra-1.3.8.tgz
tar xzvf gocr-0.50pre-patched.tgz

Compile & Install Gocr

You need to make and install the patched Gocr before you try to build Osra:

cd /tmp/OSRA/gocr-0.50pre-patched
./configure;
make libs;
sudo make all install;

This will install the patched gocr into /usr/local and copy Gocr header files to /usr/local/include/gocr. This may cause conflicts if you’ve installed gocr using another methods for instance using apt-get or aptitude. The gocr binary will be in /usr/local . If you have any problems, remove any other version of Gocr you may have build.

Before you continue to the next step, make sure the Gocr header files are installed:

$ ls /usr/local/include/gocr/
config.h*  gocr.h*  list.h*  output.h*    pgm2asc.h*  pnm.h*  unicode.h*

If you don’t see the header files, make sure you followed all the steps above.

Compile & Install Osra

Next compile Osra:

cd /tmp/OSRA/gocr-0.50pre-patched
./configure
make all

To install Osra on your system, run the following using sudo:

sudo make install

Look for it in /usr/local/bin:

/usr/local/bin/osra

Note: If you break your system while following these instructions, it’s not my fault. These are give in good faith, but if I’ve typed something wrong, too bad, I am not responsible!

/usr/local/bin/osra –version

/usr/local/bin/osra  version: 1.3.8

Updated April 12th 2012: Added libnetpbm10-dev to the list of required packaged to pre-install.
Updated April 16th 2012: Added missing build steps to Gocr section. Was missing ./configure step
Updated April 17th 2012: Added “make libs” to the Gocr build steps, and fixed typo in the quickie install section.
Updated April 20th 2012: Added libocrad-dev to list of packages to add. Note: This package is not available for Lucid!
Updated April 21st: Updated dependencies and cleaned up the document.

http://forum.lazy8studios.com/index.php?PHPSESSID=h1d37r13a2d2ccnk5c5j6b2c94&topic=475.msg837#msg837

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).

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 …

Update: I’ve a newer document that shows how to install Osra on Ubuntu 11.10 (Oneiric):

• http://timony.com/mickzblog/2012/03/24/build-install-osra-1-3-8/

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.