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augustus-software

Augustus

Augustus predicts genes in eukaryotic genomic sequences.

Information

Usage

See which versions of augustus are available:

$ module avail augustus

Load augustus

$ module load augustus/3.2.3

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.3.tar.gz
$ tar xf augustus-3.2.3.tar.gz
$ cd augustus-3.2.3
$ sed -i 's/#ZIPINPUT = true/ZIPINPUT = true/' common.mk
$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/export/apps/bamtools/2.4.0/lib LDFLAGS="$LDFLAGS -L/export/apps/bamtools/2.4.0/lib" CFLAGS="$CFLAGS -I/export/apps/bamtools/2.4.0/include"
$ sed -i 's#/usr/include/bamtools#/export/apps/bamtools/2.4.0/include#' auxprogs/bam2hints/Makefile
$ sed -i 's#/usr/include/bamtools#/export/apps/bamtools/2.4.0/include#' auxprogs/filterBam/src/Makefile
$ sudo mkdir /export/apps/augustus/3.2.3
$ sudo chown aorth /export/apps/augustus/3.2.3
$ make INSTALLDIR=/export/apps/augustus/3.2.3 install
$ sudo chown -R root:root /export/apps/augustus/3.2.3

Augustus requires bamtools, but for some reason it doesn't compile out of the box with the copy it comes with, so I told it to use the one already on our system.

augustus-software.txt · Last modified: 2017/05/23 18:08 by aorth