ILRI Research Computing

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====== Augustus ======
Augustus predicts genes in eukaryotic genomic sequences.

===== Information =====

  * Version: 3.3
  * Added: January, 2018
  * Link: http://bioinf.uni-greifswald.de/augustus/

===== Usage =====

See which versions of augustus are available:
<code>$ module avail augustus
</code>

Load one version into your environment:
<code>$ module load augustus/3.3</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.tar.gz
$ tar xf augustus-3.3.tar.gz 
$ cd augustus
$ sed -i 's/#ZIPINPUT = true/ZIPINPUT = true/' common.mk
$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/export/apps/bamtools/2.5.1/lib64 LDFLAGS="$LDFLAGS -L/export/apps/bamtools/2.5.1/lib64" CFLAGS="$CFLAGS -I/export/apps/bamtools/2.5.1/include/bamtools"
$ sed -i 's#/usr/include/bamtools#/export/apps/bamtools/2.5.1/include/bamtools#' auxprogs/bam2hints/Makefile
$ sed -i 's#/usr/include/bamtools#/export/apps/bamtools/2.5.1/include/bamtools#' auxprogs/filterBam/src/Makefile
$ sudo yum install boost-devel
$ make clean
$ make
$ sudo mkdir /export/apps/augustus/3.3
$ sudo chown aorth /export/apps/augustus/3.3
$ make INSTALLDIR=/export/apps/augustus/3.3 install
$ find /export/apps/augustus/3.3 -type d -exec chmod 755 {} \;
$ find /export/apps/augustus/3.3/config/ -type f -exec chmod 644 {} \;
$ find /export/apps/augustus/3.3/scripts -type f -exec chmod 644 {} \;
$ find /export/apps/augustus/3.3/scripts -iname '*.pl' -exec chmod 755 {} \;
$ sudo chown -R root:root /export/apps/augustus/3.3</code>

Augustus requires bamtools at compile time (but not during run time).