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config.example
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config.example
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## The config file should be set as below, offering the information what you need, whereas the other which you don't need can be ignored.
## ==>config.example<==
-----------------------------------------------------------------
[database]
ref=/share/database/hg19.fa
AP=/home/bio/software/filter_adapter/db/HiSeqAdaptersPrimersForAncientDNALibrary.fa
lncRNA=/share/database/human_lncrna.fa
rRNA=/share/database/human_all_rRNA.fasta
refGene=/share/database/refGene.gtf
refseq-bed=/share/database/hg19.refseq.bed12
gencode-gtf=/share/database/gencode.v7.annotation.gtf
gencode-gc=/share/database/gencode.v7.gc.txt
genelist=./gene_list.txt
[software]
## QC software
selectIdxFastq=/home/bio/pub/GATE/bin/selectIdxFastq.pl
mergeOverlapPE=/home/bio/pub/GATE/bin/mergeOverlapPE.pl
filterPCRdup=/home/bio/pub/GATE/bin/filterPCRdup.pl
scanAP=/home/bio/software/scanAP/scanAP
trim_seq=/home/bio/pub/GATE/bin/trim_seq.pl
fastq2pe=/home/bio/pub/GATE/bin/fastq2pe.pl
fastqcut=/home/bio/pub/GATE/bin/fastqcut.pl
SolexaQA=/usr/local/bin/SolexaQA.pl
RNA-SeQC=./software/RNA-SeQC/RNA-SeQC_v1.1.7.jar
## ALN software
bwa=/usr/local/bin/bwa
bowtie=/usr/local/bin/bowtie2
soap=/usr/local/bin/soap
maq=/usr/local/bin/maq
# BAMtools
bamtools=/usr/local/bin/bamtools
## VAR software
samtools=/usr/local/bin/samtools
picard=/usr/local/bin/picard-1.82.jar
gatk=/usr/local/bin/GenomeAnalysisTK.jar
VarScan=/usr/local/bin/VarScan.jar
## sub-setting for VarScan
filter=--min-coverage 6 --min-reads2 3 --min-reads2 5e-02
## EXP software
tophat=/usr/local/bin/tophat2
cufflinks=/usr/local/bin/cufflinks
## AS software
AlternativeSplicing=./bin/AlternativeSplicing.jar
SamToFastq=./bin/SamToFastq.jar
GenePlot=/home/bio/pub/GATE/bin/GenePlot.pl
[setting]
PATH=/home/bio/pub/GATE/bin/:/home/bio/bin/
RSeQCPATH=/usr/local/bin/
PYTHONPATH=/usr/local/lib/python2.7/site-packages
# Java config
heap=4g
# BWA alnpara
bwaaln=-n 0.05 -e 5 -d 10 -o 3 -l 25 -k 3 -t 12 -M 2
# TopHat para
tophat=--solexa-quals -p 10 -r 200 --bowtie2
# Cufflinks para
cufflinks=-p 10 -b -u --total-hits-norm
# BWA aln outdir
aln_outdir=aln
# Variation calling outdir
var_outdir=var
# scanAP penalty score matrix
align.mat=/home/bio/software/scanAP/align.mat
# trim_seq.pl para
trim_seq=-ap_db $AP -edge 3 -len_t 25 -len_p 0.25 -trim_mode both -ap_mode -verbose
# quality control outdir
qc_outdir=qc
# PBS jobs parameters
multithreads=2
qsub=-cwd -q mem.q -P mem -l cpu=8,vf=16G
[rule]
# if 'clean=yes' or 'clean=TRUE' it will clean the interval files
clean=true
# if you want to run in multi-processes mode
multimode=yes
[LIB]
#Label
LB=A
#Sample ID
ID=A
#Sample speice
SM=hs
#Sequencing platform
PL=Illumina
#Sequencing instrument/unit
PU=hiseq2000
fq1=./01.data/A-1.fq.gz
fq2=../01.data/A-2.fq.gz
[LIB]
LB=B
ID=B
SM=hs
PL=Illumina
PI=2000
PU=hiseq2000
MergePE=TRUE
fq1=./01.data/B-1.fq.gz
fq2=./01.data/B-2.fq.gz
fq=./01.data/B_SE.fq
[LIB]
LB=ST
ID=ST
SM=mm
PL=Illumina
PU=miseq
Index=CAGT
fq1=./01.data/C1-1.fq.gz
fq2=./01.data/C1-2.fq.gz
fq1=./01.data/C2-1.fq.gz
fq2=./01.data/C2-2.fq.gz
fq=./01.data/C_SE1.fq
fq=./01.data/C_SE2.fq
[INPUT]
Label=D
ref-bwabam=./02.aln/D1.bam
ref-bwabam=./02.aln/D2.bam
Label=E
ref-bwabam=./02.aln/E.bam
-----------------------------------------------------------------
## ==> PBS.example <==
-----------------------------------------------------------------
#!/bin/bash
#PBS -N mpi_template
#PBS -l nodes=1:ppn=10
#PBS -l walltime=01:40:00
#PBS -j oe
#PBS -q mem.q
NSLOTS=`cat ${PBS_NODEFILE} | wc -l`
cd $PBS_O_WORKDIR
source /public/software/mpi/openmpi1.3.4-gnu.sh
mpirun -hostfile $PBS_NODEFILE -np $NSLOTS \
/public/software/namd/namd2.7-gcc-openmpi/namd2 \
apoa1.namd >& namd.log
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