augustus-software
This is an old revision of the document!
Table of Contents
Augustus
Augustus predicts genes in eukaryotic genomic sequences.
Information
- Version: 3.2.3
- Added: May, 2017
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.1495552120.txt.gz · Last modified: 2017/05/23 15:08 by aorth