##Optionally set the path of moabs bin/ dir. It tells where to find other modules.
##The program will first find it automatically. If you explicitly define it here, the default value is over-written by your definition.
##MOABS_BIN=~/moabs/moabs-v1.3.2.src.x86_64_Linux.data/bin/
##You can also define any variable "variable=value" here and use it in this config as $variable.
##For example, you can define MOABS_ROOT=/whatever/path/ and mcall path as $MOABS_ROOT/bin/mcall.

##The leftside  is the label with '_' separating sample name, replicate name, paired-end mate(if possible)
##The rightside is the real file name corresponding to the label
[INPUT]
s1_r1=s1_r1.fq
s1_r2_1=s1_r2_1.fq
s1_r2_2=s1_r2_2.fq
s2_r1=ko_r1.fq
s2_r2_1=ko_r2_1.fq
s2_r2_2=ko_r2_1.fq


##If [INPUT] is fastq file, the first TASK is MMAP. Otherwise, it could be MCALL, MCOMP, MONE, MCALL2, MMERGE or NA.
##NA makes moabs to output all options merged from this config file and command line overrides.
##Label is ',' separated and matches (s1, s2) in the label description in [INPUT]
##Parallel could be NONE, THREAD, or QSUB
[TASK]
Program=MMAP

Label=wt,ko

Parallel=THREAD
#Parallel=QSUB
#Parallel=NONE


[QSUB]
Template=$MOABS_BIN/template_for_qsub

##For each individual program, 'Path' sets the aboslute path to the executable.
##Every other parameter can be set like p=16 for using 16 cpus.

##If you do not have mm9.fa at hand, download it at https://s3.amazonaws.com/deqiangsun/software/moabs/ref/mm9.fa.gz
##Make sure mm9.chrom.sizes exists in the same directory. Download it at https://s3.amazonaws.com/deqiangsun/software/moabs/ref/mm9.chrom.sizes

[MMAP]
Path=$MOABS_BIN/bsmap
p=16
d=~/moabs/ref/mm9.fa 

[MCALL]
Path=$MOABS_BIN/mcall
r=~/moabs/ref/mm9.fa 
p=4

[MCOMP]
Path=$MOABS_BIN/mcomp
reference=~/moabs/ref/mm9.fa
