smapDigger works on 64-bit Unix (Linux, Ubuntu, Mac OS, etc) based systems.

Hardware requirements

At least one computing node equipped with at least 10 GB Memory

Software requirements

GCC 4.6.0 or higher
Perl 5.16.3 or higher
Java 1.6.0 or higher
zlib 1.2.8 or higher

1. cd [smapDigger root directory]
2. Execute command "chmod -R 755 ./"
3. Execute command "./Software_Setup.sh"

1, Execute command "./Module_Setup.sh <Perl module path (Absolute Full Path)>" in user mode

2, Add the path of your perl module to environmental variable $PARL5LIB in file ~/.bashrc. For most linux system, it is usually something like "export PERL5LIB=$PERL5LIB:/share/perl5/:/lib64/perl5/".

3, Execute command "source ~/.bashrc"

1, Execute command "./Module_Setup.sh"

1, Download example file package "data.tar.gz" from http://gigadb.org/dataset/100143 and save it to the root directory of SMAP. Extract the package with command "tar vxzf data.tar.gz"

2, Put file "hg19.fa" into "./data/common" directory (It could also be downloaded from http://gigadb.org/dataset/100143)

3, Check if file "hg19.chr_len.bed" is in "./data/common" directory

4, Check if file "CpGIsland.bed.seq.example" and "Upstream2k.bed.seq.example" are in "./data/element" directory

5, Check if file adapter file and raw fq files are in "./data/sample" directory

6, Execute script "./Data_Prepare.sh" when use it first time.

1, modify configuration file "Eval.configure"

2, Execute script "perl ./Monitor.pl -c Eval.configure -o [Output path]"

1, cd [Output path]

2, Execute script “./SMAP_Run.sh"

2, Execute script "perl RRBS_prepare.pl"

3, Execute script "perl RRBS_asm.pl"

4, Execute script "perl RRBS_dmr.pl"

5, Execute script "./RRBS_report.sh"