defuse.sh Files

# defuse.sh
# Author: Chin-Chen Pan
# Directore, General and Surgical Pathology
# Professor, attending pathologist
# Department of Pathology and Laboratory Medicine
# Taipei Veterans General Hospital
# TAIWAN
# Version 1.3.1
# Date: Feb 22, 2016

[Introduction]

defuse.sh is a simple script to run deFuse for fusion detection. The script accepts gzip input files and is compatible with fusion_test.sh.

[Before running]

1. Prepare defuse.config. The file contains four words in one line. No other words and lines are allowed.

	/path/to/programs /path/to/inputfile /path/to/outputfile thread_number

	ex1: 
	/home/user_name	/media/user_name/disk1/input /home/user_name/output 8

	ex2:
        ~  ~/input ~/output 8

2. R, R package ada must be installed.

        sudo apt-get install r-base
        R
        >install.packages("ada")
        >q()

3. Install gmap. Please refer to the authors' websites.
   If you place the folders of gmap-2016-06-30 in the /path/to/programs, the script can automatically install the programs the first time you run it.
   Download prebuilt defuse (including required binaries) from this site and extract the files to /path/to/programs/defuse.
   The script will automatically download reference files and build the index files to /path/to/programs/defuse_ref. The final size is around 115G and it may take more than 10 hours to build the index.
        

4. The followings files and folders must be placed in the /path/to/programs.

	defuse
        defuse_ref

   The original configuration files, ./defuse/scripts/config.txt is used as template. Do not change its content. You can create a secondary configuration file config2.txt.
	   
5. The seq files must be paired end, and named as samplename_1.suffix and samplename_2.suffix. The suffix must be one of the fastq/fq/fastq.gz/fq.gz.

6. In order to be compatible with SOAPfuse, the seq files must be placed in the following paths:

	/path/to/inputfile/samplename/Lib/samplename_1.suffix
	/path/to/inputfile/samplename/Lib/samplename_2.suffix

[RUNNING]

Syntax:  sh defuse.sh samplename suffix -options
	
	options:
	
	-df2: use secondary configuration file
        -s: shutdown after finished
	-kt: keep temporary files
	
	ex1:
	  sh defuse.sh test1 fastq.gz 
	ex2:
	  sh defuse.sh test2 fastq -kt -s