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
- bamtools
- I needed this when installing version 2.5.5 under Fedora
- $ sudo yum install libstdc++-static glibc-static
Installation
- $ ver="3.2.1"
- $ cd /programinstallers/
- $ wget -N http://bioinf.uni-greifswald.de/augustus/binaries/augustus-$ver.tar.gz
- $ cd /usr/local/bin
- $ tar -zxvf /programinstallers/augustus-$ver.tar.gz
- Version 3.3: $ mv augustus augustus-$ver
- Make a version-independent symlink
$ ln -s augustus-$ver augustus
- $ cd augustus/src
- 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
- $ make
- Create a global configuration directory for Augustus
$ sudo mkdir /etc/augustusconfig
- $ sudo chmod 777 /etc/augustusconfig
- 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
…
- Move documentation to web page
$ mv retraining.html docs /programinstallers/web/augustus/
- Optional cleanup of source code to save some space
$ rm src include -rf