This page was last updated on Friday, 19-May-2023 09:48:04 CDT
Installation notes for TopHat version 2.0.12
Home Page
Prerequisites
None
Installation
- $ ver="2.0.12"
- $ cd /programinstallers/
- $ wget -N http://ccb.jhu.edu/software/tophat/downloads/tophat-$ver.Linux_x86_64.tar.gz
- $ cd /usr/local/bin
- $ tar -zxvf /programinstallers/tophat-$ver.Linux_x86_64.tar.gz
- Make a version-independent symlink. First remove old one if present
$ rm tophat
- Then make symlink
$ ln -s tophat-$ver.Linux_x86_64 tophat
- Add binaries to default PATH for all users
$ sudo nano /etc/profile
...
PATH="$PATH:/usr/local/bin/tophat"
...
- 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