Getting BioPerf to execute

Upon executing script to start BioPerf, the following error came up:
$ ./use-bioperf.sh
You can do the following:
[R] Run BioPerf
[I] Install BioPerf on your architecture
(if your architecture is not PowerPc, x86)
[C] Clean outputs in $HOME/BioPerf/Outputs
[D] Display all versions of the installed codes
R
Please specify your architecture
[A] Alpha
[P] PowerPC
[X] x86
[H] Custom. (If you have already ran the install-codes.sh successfully
to completion, you can choose this option to run the binaries installed
on your system)
X
$HOME/BioPerf/Scripts/Run-scripts/run-bioperf.sh: line 21: syntax error near unexpected token `('
$HOME/BioPerf/Scripts/Run-scripts/run-bioperf.sh: line 21: ` echo There is no directory named $HOSTNAME-Binaries (created by install-codes.sh) in $BIOPERF/Binaries '


In order to get passed this, file $HOME/BioPerf/Scripts/Run-scripts/run-bioperf.sh should be edited on line 21 to replace parentheses with curly brackets (or similar or escaped). The same should be done on line 26 because parentheses are used there as well and are not escaped.

BLAST performance analysis configuration

All the files needed for BLAST performance testing (e.g., perl scripts, databases, different versions of BLAST software, ...) are located under my account on everest under ~/BLASTanalysis.
In order to run a BLAST test, a properties file (e.g., propertyFile) needs to be edited/provided. Properties file specifies the following data: database, input file, program, I/O params are specified, number of fragments and threads, and execution host.
Once configured, run run.pl script. This script will split the input file into specified number of fragments, generate LRM scripts, and submit the job:
perl run.pl {properties file}

Formatting database for BLAST

Unformatted databases can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/, while formatted ones from ftp://ftp.ncbi.nlm.nih.gov/blast/db/.
Command to use to format a database:
formatdb -i input_db -p F -o T for nucleotide
formatdb -i input_db -p T -o T for protein

For yeast.nt use: formatdb -i yeast.nt -p T -o T
For nr use: formatdb -i nr -p T -o T