RSeqMule 0.03a

What's new: 

TO DO
- Remove locale for bundle
- Check for fortran compiler (gfortran)
- Upgrade java - temporary
- Change deployment type - other libraries
- Add check the integrity of files
- Fix dependencies
    SAMTools: NCURSES
- Fix internal error
    STAR
    Cuffdiff output: ERR stream
- Add R and R based tools
- Add cummerbund / igv
- cuffdiff: /usr/lib64/libz.so.1: no version information available
- Check error stream
- better progress and VERBOSE mode for long compiling (ex. R)
- mode for exclude tools (for shorter install process)
- check python version - directory

 Version 0.0.3
- Add Java version check -- test?
- Move all directory strings to property file
- Move all outputs to temp directory
- Modify sources for GCC 4.7
    Add #include <unistd.h>
- Fix aligner specific
    TOPHAT: re-use transcriptome index for faster alignment
    PERM: fix execution error when the command include parenthesis
    PERM: remove L and S flag with single ended input
- Test download                 - PASS
- Test script STAR-CUFFDIFF     - PASS
- Test script PERM-CUFFDIFF     - PASS
- Test script TOPHAT-CUFFDIFF   - PASS
- Test run STAR-CUFFDIFF
- Test run PERM-CUFFDIFF
- Test run TOPHAT-CUFFDIFF

- Add sample file from Galaxy
- Fix compile module
    configure

Version 0.0.2
- Now you can run 3 aligners and 1 DE calculator combinations with FastQC.
- New tools
    PerM
    FastQC
- New function
    Check tools are properly installed before running analysis
- New options
    --notest : Skip the QC test.
    --script : Generate script only. You can run it later separately.
- Fix dependencies
    Add path environments for TopHat
    Bowtie2 for TopHat
- Fix the uncompress module
    Add unzip function
    Fix untar when it doesn't contain any directory in it
    Fix untar with file permission error
    Add symbolic link fix for genome.fa file
- Fix minor typos
- Change the name to RSeqMule

Version 0.0.1
- Initial release (alpha)