Warning
Iceberg was decommissioned on 30th November 2020. Users of Iceberg need to switch to using ShARC and/or Bessemer instead.
ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).
After connecting to Iceberg (see Establishing a SSH connection), start an interactive session with the qsh or qrsh command.
To add the annovar binaries to the system PATH, execute the following command
module load apps/binapps/annovar/2015DEC14
The annovar manual is available online at http://annovar.openbioinformatics.org/en/latest/
The install is a collection of executable Perl scripts. Installation involves copying the directory and adding it to the PATH. It seems that annovar uses dates to distinguish between releases rather than version numbers
tar -xvzf ./annovar.latest.tar.gz
mkdir -p mkdir -p /usr/local/packages6/apps/binapps/annovar
mv annovar /usr/local/packages6/apps/binapps/annovar/2015DEC14
The module file is on the system at /usr/local/modulefiles/apps/binapps/annovar/2015DEC14
Its contents are
#%Module1.0#####################################################################
##
## annovar modulefile
##
## Module file logging
source /usr/local/etc/module_logging.tcl
##
proc ModulesHelp { } {
puts stderr "Makes annovar 2015DEC14 available"
}
set ANNOVAR_DIR /usr/local/packages6/apps/binapps/annovar/2015Dec14
module-whatis "Makes annovar 2015DEC14 available"
prepend-path PATH $ANNOVAR_DIR