This page was last updated on Wednesday, 18-Feb-2026 14:05:53 CST

Installation notes for Nextflow

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Prerequisites

Java 17 or later

1. sudo apt-get install default-jdk
2. sudo apt-get install openjdk-25-jdk

Installation

1. $ ver="2.0.12"
2. $ cd /programinstallers/
3. $ wget -N http://ccb.jhu.edu/software/tophat/downloads/tophat-$ver.Linux_x86_64.tar.gz
4. $ cd /usr/local/bin
5. $ tar -zxvf /programinstallers/tophat-$ver.Linux_x86_64.tar.gz
6. Make a version-independent symlink. First remove old one if present
   $ rm tophat
7. Then make symlink
   $ ln -s tophat-$ver.Linux_x86_64 tophat
8. Add binaries to default PATH for all users
   $ sudo nano /etc/profile
   ...
   PATH="$PATH:/usr/local/bin/tophat"
   ...
9. Edit any python script to explicitly use python2 since TopHat does not support python3
   grep -nr python

   tophat:1:#!/usr/bin/env python2
   tophat-fusion-post:1:#!/usr/bin/env python2
   contig_to_chr_coords:1:#!/usr/bin/env python2
   sra_to_solid:1:#!/usr/bin/env python2
   bed_to_juncs:1:#!/usr/bin/env python2