T-Coffee & Co

Installing T-Cofee, ClustalW and SAP

1. Download and install CLUSTALW

ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/

Example:

wget ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw1.83.linux.tar.gz
tar xvfz clustalw1.83.linux.tar.gz
cd clustalw1.83.linux
cp makefile.linux makefile
make
cd ..
sudo mv clustalw1.83.linux /usr/local/src/clustalw1.83
sudo ln -s /usr/local/src/clustalw1.83/clustalw /usr/local/bin/

There may be a more elegant way. I just didn't find it yet. Clustalw is also available as Ubuntu package clustalw.

2. Download and install SAP

download and unpack and compile the non-official SAP distribution, for example:

wget http://biskit.pasteur.fr/install/troubleshooting/sap_repackaged
tar zxvf sap_repackaged
cd sap_distribution/source
make sap

link or copy sap into your path, for example:
```
sudo cp ../bin/sap /usr/local/bin
```
Note:

The source code for SAP is "freely available for non-profit academic work" from Willie Taylor's ftp folder:

ftp://mathbio.nimr.mrc.ac.uk/pub/wtaylor/sap and ftp://mathbio.nimr.mrc.ac.uk/pub/wtaylor/util

Cederic Notredame kindly sent us is own re-packaged version for easier compilation.

3. Download and install T-COFFEE

http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html

For example(please adapt the download link):

wget http://www.tcoffee.org/Packages/Stable/Latest/\
/T-COFFEE_distribution_Version_9.01.tar.gz

tar zxvf T-COFFEE_distribution*.tar.gz
rm T-COFFEE_distribution*.tar.gz
sudo mv T-COFFEE_distribution_Version* /usr/local/src

cd /usr/local/src/T-COFFEE_distribution_Version*
sudo ./install t_coffee

cd /usr/local/bin
sudo ln -s ../src/T-COFFEE_distribution_Version*/bin/binaries/linux/t_coffee .

Ensure that all folders in the newly created ~/.t_coffee belong to your user (replace raik:users by your own login and group name):

cd
sudo chown -R raik:users .t_coffee

Note:

An outdated version of T-Coffee is also available as Ubuntu package t-coffee

4. Configure Biskit & T-Coffee

option 1: via the biskit exe_t_coffee.dat config file:

make a local copy of the Biskit Executor configuration for T-Coffee:
```
cp biskit/Biskit/data/defaults/exe_t_coffee.dat ~/.biskit/
```

adapt the parameters:

[BINARY]
bin = /path/to/t_coffee  ## if not in $PATH
...
[ENVIRONMENT]
CLUSTALW_4_TCOFFEE = /path/to/clustalw
SAP_4_TCOFFEE = /path/to/sap
... # more env. variables are optional (see below)

option 2: via normal environment variables (works also w/o biskit)
- make sure t_coffee is in your $PATH
- setenv CLUSTALW_4_TCOFFEE /path/to/clustalw
- setenv SAP_4_TCOFFEE /path/to/sap
Optional settings
- force T-Coffee not to validate filenames of structures against the RCSB. The validation is quite time consuming, therefore this setting is recommended. setenv NO_REMOTE_PDB_DIR 1
- If you have a local database installed this can be used for the validation. setenv PDB_DIR /path/to/your/pdb/database

5. Test T-Coffee / SAP / ClustalW

Execute the Biskit unittest:
```
cd biskit/Biskit/Mod
python Aligner.py
```
This should (after some time and a lot of other output) result in something like this:
```
...
The alignment result is in /tmp/tmp1SewRJ_test_Aligner/t_coffee
ok

----------------------------------------------------------------------
Ran 2 tests in 99.918s

OK
```
Note:
The test result is by default deleted. In order to prevent this, you can change the last line in Aligner.py (works for any other Biskit module) to:
```
BT.localTest(debug=1)
```
Problems? See also: T-Coffee troubleshooting!

Usage:

see Biskit.Mod.Aligner
see scripts/Mod/align.py

Custom configuration:

see biskit/external/defaults/exe_t_coffee.dat

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