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config-luna.txt
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config-luna.txt
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##############################################
## The code can run in both hal and luna. These are the settings
## to run the pipeline in luna (Human genome as reference). Please
## don't use this configuration file for other species.
##########################################
## Paths & meta data files
##########################################
gtex_path = /ifs/e63data/schultzlab/wangq/rna-seq-normal/gtex
tcga_path = /ifs/e63data/schultzlab/wangq/rna-seq-normal/tcga
gtex_sample_attr = phs000424.v5.pht002743.v5.p1.c1.GTEx_Sample_Attributes.GRU.txt
##########################################
## Third-party tools
##########################################
fastqc_bin = /ifs/e63data/schultzlab/bin/FastQC/fastqc
bedtools_dir = /opt/common/CentOS_6/bedtools/bedtools-2.22.0/bin
rsem_dir = /ifs/e63data/schultzlab/bin/rsem-1.2.20
ubu_dir = /ifs/e63data/schultzlab/bin/ubu-1.2/
star_bin = /ifs/e63data/schultzlab/wangq/bin/STAR-STAR_2.4.2a/bin/Linux_x86_64_static/STAR
rseqc_dir = /ifs/e63data/schultzlab/bin/RSeQC-2.6.1/opt/common/CentOS_6/python/python-2.7.8/bin
picard_dir = /opt/common/CentOS_6/picard/picard-tools-1.129
sratool_dir = /ifs/e63data/schultzlab/bin/sratoolkit.2.5.2-centos_linux64/bin
mRIN_dir = /ifs/e63data/schultzlab/bin/mRIN
##########################################
## Reference files indexed for aligners
##########################################
ref_fasta = /ifs/depot/assemblies/H.sapiens/hg19/hg19.fasta
gencode = /ifs/e63data/schultzlab/wangq/ref/hg19/gencode.v19.annotation.gtf
index_rsem = /ifs/e63data/schultzlab/wangq/ref/hg19/rsem-index/hg19
index_star = /ifs/e63data/schultzlab/wangq/ref/hg19/star-index
house_keeping_genes = /ifs/e63data/schultzlab/wangq/ref/hg19/hg19.HouseKeeping-LongGenes.bed
ENSG_UCSC_common_genes = /ifs/e63data/schultzlab/wangq/ref/hg19/gencode.v19_ucsc.known.txt
##########################################
## Machine specific
##########################################
cluster = luna
thread_no = 8
memory = 40
wall_time = 40