http://code.google.com/p/cutadapt/source/browse/trunk/README

One of the researcher reported getting very poor and inconsistent results from clipping function of FastX toolkit (to remove adapter sequences from reads). Installed cutadapt as there are better reviews of cutadapt for this purpose

Usage

module load python/2.7.1-shared
OR
module load python/2.7.1
OR
module load python/3.1.4

Installation

mkdir -p /sw/bioinformatics/cutadapt/1.0/src
cd /sw/bioinformatics/cutadapt/1.0/src
tar -zxvf cutadapt-1.0.tar.gz
cd cutadapt-1.0

python/2.7.1-shared

module purge
module load python/2.7.1-shared
python setup.py build 
python setup.py install  


>>>>>>>>>>>>>>>>>
 python setup.py build
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/cutadapt
copying lib/cutadapt/__init__.py -> build/lib.linux-x86_64-2.7/cutadapt
copying lib/cutadapt/seqio.py -> build/lib.linux-x86_64-2.7/cutadapt
copying lib/cutadapt/qualtrim.py -> build/lib.linux-x86_64-2.7/cutadapt
copying lib/cutadapt/xopen.py -> build/lib.linux-x86_64-2.7/cutadapt
copying lib/cutadapt/align.py -> build/lib.linux-x86_64-2.7/cutadapt
running build_ext
building 'cutadapt.calign' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/lib
creating build/temp.linux-x86_64-2.7/lib/cutadapt
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/sw/python/2.7.1-shared/include/python2.7 -c lib/cutadapt/calignmodule.c -o build/temp.linux-x86_64-2.7/lib/cutadapt/calignmodule.o
gcc -pthread -shared build/temp.linux-x86_64-2.7/lib/cutadapt/calignmodule.o -L/sw/python/2.7.1-shared/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cutadapt/calign.so
running build_scripts
creating build/scripts-2.7
copying and adjusting cutadapt -> build/scripts-2.7
changing mode of build/scripts-2.7/cutadapt from 644 to 755

>>>>>>>>>>>>>>>>>

python/2.7.1

cd /sw/bioinformatics/cutadapt/1.0/src
tar -zxvf cutadapt-1.0.tar.gz
cd cutadapt-1.0
module purge
module load python/2.7.1
python setup.py build 
python setup.py install  

>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 python setup.py build
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/cutadapt
copying lib/cutadapt/__init__.py -> build/lib.linux-x86_64-2.7/cutadapt
copying lib/cutadapt/seqio.py -> build/lib.linux-x86_64-2.7/cutadapt
copying lib/cutadapt/qualtrim.py -> build/lib.linux-x86_64-2.7/cutadapt
copying lib/cutadapt/xopen.py -> build/lib.linux-x86_64-2.7/cutadapt
copying lib/cutadapt/align.py -> build/lib.linux-x86_64-2.7/cutadapt
running build_ext
building 'cutadapt.calign' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/lib
creating build/temp.linux-x86_64-2.7/lib/cutadapt
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/sw/python/2.7.1/include/python2.7 -c lib/cutadapt/calignmodule.c -o build/temp.linux-x86_64-2.7/lib/cutadapt/calignmodule.o
gcc -pthread -shared build/temp.linux-x86_64-2.7/lib/cutadapt/calignmodule.o -o build/lib.linux-x86_64-2.7/cutadapt/calign.so
running build_scripts
creating build/scripts-2.7
copying and adjusting cutadapt -> build/scripts-2.7
changing mode of build/scripts-2.7/cutadapt from 644 to 755


>>>>>>>>>>>>>>>>>>>>>>>>>>>>

python/3.1.4

cd /sw/bioinformatics/cutadapt/1.0/src
tar -zxvf cutadapt-1.0.tar.gz
cd cutadapt-1.0
module purge
 module load python/3.1.4
python setup.py build 
python setup.py install  
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 python setup.py build
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.1
creating build/lib.linux-x86_64-3.1/cutadapt
copying lib/cutadapt/__init__.py -> build/lib.linux-x86_64-3.1/cutadapt
copying lib/cutadapt/seqio.py -> build/lib.linux-x86_64-3.1/cutadapt
copying lib/cutadapt/qualtrim.py -> build/lib.linux-x86_64-3.1/cutadapt
copying lib/cutadapt/xopen.py -> build/lib.linux-x86_64-3.1/cutadapt
copying lib/cutadapt/align.py -> build/lib.linux-x86_64-3.1/cutadapt
running build_ext
building 'cutadapt.calign' extension
creating build/temp.linux-x86_64-3.1
creating build/temp.linux-x86_64-3.1/lib
creating build/temp.linux-x86_64-3.1/lib/cutadapt
gcc -pthread -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/sw/python/3.1.4/include/python3.1 -c lib/cutadapt/calignmodule.c -o build/temp.linux-x86_64-3.1/lib/cutadapt/calignmodule.o
gcc -pthread -shared build/temp.linux-x86_64-3.1/lib/cutadapt/calignmodule.o -o build/lib.linux-x86_64-3.1/cutadapt/calign.so
running build_scripts
creating build/scripts-3.1
copying and adjusting cutadapt -> build/scripts-3.1
changing mode of build/scripts-3.1/cutadapt from 644 to 755
>>>>>>>>>>>>>>>>>>>>>>>>>>>>