How to install TOPCONS on local

TOPCONS is one of the many tools available used for transmembrane prediction in GPCRs. It uses prediction by several other prediction methods (scampi-msa, scampi-seq, prodiv, octopus, and pro) and based on which it, spits out the consensus topology.
Length of each predicted transmembrane helix is 21.

I have had a tough time installing TOPCONS. It had a huge number of dependencies. I thought sharing and contributing might help someone.

Instructions:

$ svn ls  https://svn.sbc.su.se/repos/cbr/modhmm-projects/trunk/install_topcons.sh

Run the above command to see install_topcons.sh on command prompt. If you do not see, then can be an issue with the SVN version you are using.

To download the package mentioned at https://svn.sbc.su.se/repos/cbr/modhmm-projects/trunk/cmdline/
Use:
svn co https:

Prerequisites for installation:
- SVN, bash, Linux environment

- NCBI old blast. Old blast has binaries for blastall and formatdb.
 Add this into your PATH or put into your bin.

- Few libraries: I missed the track of them. You will be prompted while installation.

- MEMSAT. Add this into your PATH or put into your bin. To download go to:
http://bioinfadmin.cs.ucl.ac.uk/downloads/memsat/

- TOPPRED. Add this into your PATH or put into your bin. To download go to:
http://casio.fos.su.se/misc/download/toppred.tar.gz

To install 
Run the following command
~/install_topcons.sh ~/path_to_install

It will prompt for any missing libraries that have not been installed.
I had installed to the ~/home/bin. If you do not provide any path, then all installations will be done at /usr/some_path

How to Run:
After installation, you will see catfasta.py and run_topcons.sh file inside the a bin folder of the path where installation was run. Ex:

~/install_script.sh ~/path

~/path/bin -> you will find 2 above mentioned files.

 Now to run TOPCONS: 
./run_topcons.sh fasta-seq-file [-outpath DIR]

[-output DIR], it is optional, by default the output will be in current working directory. After successful run, you will get *.txt in the out path and also one *.err file.

If you want to run TOPCONS without moving the files (catfasta.py and run_topcons.sh) from ~/path/bin folder, then the above command is perfect to run TOPCONS locally. However, you want to remove the files to your ~/path, then use:

$ run_topcons.sh test.fa -outpath outdir -topcons ~/var/www/topcons.cbr.su.se/docroot/topcons/

Interests:
I declare that I have no interests in making this or any other tool available for transmembrane prediction popular. I wrote this article voluntarily and after getting a confirmation from author's student.

I would like to thank the authors and students of TOPCONS for their tremendous patience and help.

References:
- TOPCONS: consensus prediction of membrane protein topology
Andreas Bernsel, Håkan Viklund, Aron Hennerdal and Arne Elofsson


Location: Atlanta, GA, USA

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