This page was last updated on Saturday, 26-Mar-2016 10:36:59 CDT

Installation notes for Cufflinks version 2.2.1

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Installation (compiled binary)

1. $ ver="2.2.1"
2. $ cd /programinstallers/
3. $ wget -N http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-$ver.Linux_x86_64.tar.gz
4. $ cd /usr/local/bin
5. $ tar -zxvf /programinstallers/cufflinks-$ver.Linux_x86_64.tar.gz
6. Make a version-independent symlink. First remove old one if present
   $ rm cufflinks
7. Then make symlink
   $ ln -s cufflinks-$ver.Linux_x86_64 cufflinks
8. Add binaries to default PATH for all users
   $ sudo nano /etc/profile
   …
   PATH="$PATH:/usr/local/bin/cufflinks"
   …

Prerequisites

Install from source directions

• Boost
• Samtools
  cufflinks expects libraries in a particular way, so
  1. sudo mkdir /usr/local/include/bam
  2. sudo ln -s /usr/lib/samtools /usr/local/include/bam/lib
  3. sudo ln -s /usr/lib/samtools /usr/local/include/bam/include
• Eigen
  1. ever="3.2.5"
  2. wget -N http://bitbucket.org/eigen/eigen/get/$ever.tar.gz
  3. tar -zxvf $ever.tar.gz
  4. sudo cp -puvr eigen-eigen-bdd17ee3b1b3/Eigen /usr/local/include/
  5. rm eigen-eigen-bdd17ee3b1b3 -rf

Installation

1. $ cd /programinstallers/
2. $ git clone https://github.com/cole-trapnell-lab/cufflinks.git
3. $ cd cufflinks
4. $ ./autogen.sh
5. $ ./configure --with-bam="/usr/lib/samtools"
6. $
7. $
8. $
9. $