GitHub - vmaselli/TrapCluster

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Name		Name	Last commit message	Last commit date
Latest commit History 40 Commits
bin		bin
data		data
modules/Bio		modules/Bio
scripts		scripts
sql		sql
t		t
README		README
antisense.url		antisense.url
trapcluster_conf.pl		trapcluster_conf.pl
trapcluster_conf.sample.pl		trapcluster_conf.sample.pl

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This is the UniTrap project.

To work properly you need to 

1. setup the enviroment variable 
'Unitrap' - should point to your Unitrap root directory
'Blastdir' - should point to where your BLAST databases can be found (if you want to run Blast)

Example for bash shell:
Unitrap=$HOME/your_dir/UniTrap
Blastdir=$HOME/your/path/for/blast/genome';

2. add the modules directory of Unitrap to your PERL5 lib
export Unitrap
export PERL5LIB=$PERL5LIB:$Unitrap/modules
Example for t- c- shell
setenv Unitrap $HOME/your_dir/UniTrap
setenv PERL5LIB ${PERL5LIB}:/$Unitrap/modules

3. change unitrap_conf.sample.pl in unitrap_conf.pl

#Requirements
4. be sure that you have

	EnsEMBL api - NOTE: currently tested with v58
	BioPerl api - NOTE: use the Ensembl-compatible version, i.e. bioperl 1.2.3 : http://bioperl.org/DIST/old_releases/bioperl-1.2.3.tar.gz
	Blast
	Blat
	Mysql Database
	perl modules: DBD, DBI
	IO::String
## TO START ##

#TEST


#Mysql Setup
	1. set the config file to access to the database
	2. run the script: scripts/create_database.pl

#IMPORT TRAP FROM THE BEGINNING
run load_trap.pl