INSTALL

http://homer.salk.edu/homer/introduction/install.html#Installing_3rd_Party_Software

The commands gs, seqlogo, blat, and samtools should now work from the command line (if they don't and you think they should, remember to type: source ~/.bash_profile)

Introduction

ASSA is a pipeline for large scale RNA-RNA interaction prediction that utilizes thermodymanics tools from the RNAstructure package.

Prerequisites

To use ASSA, you will need to install:

• blastn: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
• Fold and bifold tools (text interfaces) from the RNAstructure package: http://rna.urmc.rochester.edu/Overview/index.html
  • Don't forget to set the DATAPATH environment variable: http://rna.urmc.rochester.edu/Text/Thermodynamics.html
• R: https://www.r-project.org/
• Statistics::R Perl module
• You will also need to have Perl intalled

ASSA Installation Instructions

1) Make sure that you have ~/bin (where ~ is your home directory) in your $PATH environment variable by typing "echo $PATH".
If it is not there add the following line in your ~/.bash_profile and type "source ~/.bash_profile":
export PATH=$PATH:$HOME/bin

2) Add the ~/bin folder (or any other location) to the list of directories for Perl modules.
Add the following line in your ~/.bash_profile and type "source ~/.bash_profile":
export PERL5LIB=$PERL5LIB:$HOME/bin

3) Install ASSA:
unzip assa-0.01.zip
cd assa-0.01
chmod a+x assa.pl
mv -v assa.pl ASSA ~/bin

4) To test that ASSA is installed properly just type 'assa.pl' and you will see version and usage message

5) To make sure that RNAstrucrure tools have been installed properly you can type:
Fold _7SL.fna _7SL.ct

5) To run ASSA on the sample sequences using 4 CPUs you can type:
assa.pl _7SL.fna _TP53.fna > _out.assa

Enabling more ASSA options

You may want to install the following items to enable additional ASSA options:

• To enable HTML-based ouput in ASSA (--html option) you will need the following Perl modules:

  • HTML::Template
  • Bio::Perl
  • Bio::Graphics

• To enable automatic masking of Alu repeas (--filter_alu option) you will need to install:

  • RepeatMasker: http://www.repeatmasker.org/RMDownload.html

IMPORTANT NOTES

The transcript sequences you provide as input to assa.pl must consist of ACGT symbols ONLY.
No other letters (such as N) are allowed.