Carrot root and DNA VCRU Bioinformatics USDA ARS Vegetable Crops Research Unit

This page was last updated on Sunday, 22-Oct-2017 21:19:28 CDT

Installation notes for Augustus version 3.2.1

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Prerequisites

Installation

  1. $ ver="3.2.1"
  2. $ cd /programinstallers/
  3. $ wget -N http://bioinf.uni-greifswald.de/augustus/binaries/augustus-$ver.tar.gz
  4. $ cd /usr/local/bin
  5. $ tar -zxvf /programinstallers/augustus-$ver.tar.gz
  6. Version 3.3: $ mv augustus augustus-$ver
  7. Make a version-independent symlink
    $ ln -s augustus-$ver augustus
  8. $ cd augustus/src
  9. Not needed with 3.3: Bamtools is not where the Makefile expects, so do this first for each of bam2hints filterBam/src
    $ nano auxprogs/bam2hints/Makefile

    INCLUDES = /usr/local/include/bamtools
    LIBS = -L/usr/local/lib/bamtools -lbamtools -lz
  10. $ make
  11. Create a global configuration directory for Augustus
    $ sudo mkdir /etc/augustusconfig
  12. $ sudo chmod 777 /etc/augustusconfig
  13. Add programs and scripts to default PATH, and config to environment
    $ sudo nano /etc/profile

    PATH="$PATH:/usr/local/bin/augustus/bin:/usr/local/bin/augustus/scripts:/usr/local/bin/augustus/auxprogs"

    export AUGUSTUS_CONFIG_PATH=/etc/augustusconfig
  14. Move documentation to web page
    $ mv retraining.html docs /programinstallers/web/augustus/
  15. Optional cleanup of source code to save some space
    $ rm src include -rf