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snake_conf.yaml
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snake_conf.yaml
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#
# This is the Snakemake configuration file that specifies paths and
# and options for the mapping pipeline
#
{
# py2 is a hack so that python2 scripts can be called
# by snakemake (which is written in python3). The value should
# be a command to do whatever is needed to setup a python2 environment and
# call the python2 interpreter. Depending on your system configuration,
# this might involve setting the PATH environment variable or
# just calling python2
"py2" : "PATH=$HOME/anaconda2/bin:$PATH; python ",
# WASP directory containing scripts
"wasp_dir" : "/iblm/netapp/home/gmcvicker/proj/WASP",
# directory to write all output data files to
"output_dir" : "/iblm/netapp/home/gmcvicker/data1/external/Grubert2015/WASP",
# location of chromInfo file containing chromosome names and lengths
# (can be downloaded from UCSC genome browser)
"chrom_info" : "/iblm/netapp/home/gmcvicker/proj/WASP/examples/example_data/chromInfo.hg19.txt",
# directory to read VCF files from (used to write SNP input files)
"vcf_dir" : "/iblm/netapp/home/gmcvicker/data1/external/1000Genomes/GRC37/20130502",
# OLD way: directory to write SNP plain text input files to
"snp_dir" : "/iblm/netapp/home/gmcvicker/proj/WASP/examples/example_data/genotypes/snps",
# directory to write SNP HDF5 input files to
snp_h5_dir : "/iblm/netapp/home/gmcvicker/proj/WASP/examples/example_data/genotypes/snp_h5",
# path to samtools
"samtools" : "/iblm/netapp/home/gmcvicker/anaconda2/bin/samtools",
# path to bowtie2 aligner
"bowtie2" : "/iblm/netapp/home/gmcvicker/anaconda2/bin/bowtie2",
# prefix for bowtie2 reference genome index
"bowtie2_index" : "/iblm/netapp/data1/external/GRC37/combined/bowtie2_index/hg37",
# sample file containing sample names and paths to fastq files
"sample_file" : "/iblm/netapp/data1/external/Grubert2015/sample_paths_H3K27ac.1000G_only.txt"
}