This page was last updated on Sunday, 10-Jul-2016 09:17:25 CDT

Installation notes for Trinity version 2.1.1

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Prerequisites

GMAP GSNAP for genome-guided Trinity

Installation

1. $ ver="2.1.1"
2. $ cd /programinstallers/
3. $ wget -N https://github.com/trinityrnaseq/trinityrnaseq/archive/v$ver.tar.gz
4. $ mv v$ver.tar.gz trinityrnaseq-$ver.tar.gz
5. $ cd /usr/local/bin
6. $ tar -zxvf /programinstallers/trinityrnaseq-$ver.tar.gz
7. $ cd trinityrnaseq-$ver
8. $ make
   …
   

   Performing Unit Tests of Build
    
   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   JellyFish:               has been Installed Properly
   Inchworm:                has been Installed Properly
   Chrysalis:               has been Installed Properly
   QuantifyGraph:           has been Installed Properly
   GraphFromFasta:          has been Installed Properly
   ReadsToTranscripts:      has been Installed Properly
   fastool:                 has been Installed Properly
   parafly:                 has been Installed Properly
   samtools-0.1.19          has been Installed Properly

9. $ cd ..
10. If upgrading:
    $ rm trinityrnaseq
11. Make a version-independent symlink
    $ ln -s trinityrnaseq-$ver trinityrnaseq
12. Add to default PATH for all users
    $ sudo nano /etc/profile
    …
    PATH="$PATH:/usr/local/bin/trinityrnaseq"
    …
13. Not sure if this helps, but make a symlink to TransDecoder in the Trinity plugins folder
    $ cd /usr/local/bin/trinityrnaseq/trinity-plugins
14. $ ln -s /usr/local/bin/TransDecoder