Cufflinks 설치

1. Installing Boost

http://isbyeon.tistory.com/entry/Boost-C-Libraries-%EC%84%A4%EC%B9%98

2. Installing the SAM tools

http://isbyeon.tistory.com/entry/SAMtools-%EC%84%A4%EC%B9%98

3. Installing the Eigen libraries

다운로드 : http://eigen.tuxfamily.org/index.php?title=Main_Page

설치 : 

방법1)

# wget http://bitbucket.org/eigen/eigen/get/3.1.2.tar.bz2

# tar jxvfp 3.1.2.tar.bz2

# export CFLAGS="-I/usr/local/src/eigen-eigen-6e7488e20373/"

 

방법2)

# yum install cmake

# wget http://bitbucket.org/eigen/eigen/get/3.1.2.tar.bz2

# tar jxvfp 3.1.2.tar.bz2

# cd eigen-eigen-5097c01bcdc4/

# mkdir build

# cd build

# cmake ../

# make install

# mv /usr/local/include/eigen3/* /usr/local/include

 

4. Building Cufflinks

다운로드 : http://cufflinks.cbcb.umd.edu/

설치 : 

# cd /usr/local/src

# wget http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.0.2.tar.gz

# tar zxvfp cufflinks-2.0.2.tar.gz

# cd cufflinks-2.0.2

# ./configure --prefix=/usr/local/cufflinks-2.0.0 --with-boost=/usr/local/boost_1_49_0/ --with-eigen=/usr/local --with-bam=/usr/local/bam/

# make && make install

# echo "export PATH=/usr/local/cufflinks-2.0.0/bin/:\$PATH" >> /etc/profile

# source /etc/profile

# which cufflinks 

/usr/local/cufflinks-2.0.0/bin/cufflinks

5. Testing the installation

# wget http://cufflinks.cbcb.umd.edu/downloads/test_data.sam

# cufflinks ./test_data.sam

You are using Cufflinks v2.0.0, which is the most recent release.

[bam_header_read] EOF marker is absent. The input is probably truncated.

[bam_header_read] invalid BAM binary header (this is not a BAM file).

File ./test_data.sam doesn't appear to be a valid BAM file, trying SAM...

[16:54:44] Inspecting reads and determining fragment length distribution.

> Processed 1 loci.                            [*************************] 100%

Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges.  It is recommended that correct parameters (--frag-len-mean and --frag-len-std-dev) be provided.

> Map Properties:

> Normalized Map Mass: 102.50

> Raw Map Mass: 102.50

> Fragment Length Distribution: Truncated Gaussian (default)

>               Default Mean: 200

>            Default Std Dev: 80

[16:54:44] Assembling transcripts and estimating abundances.

> Processed 1 loci.                            [*************************] 100%