
## Absolute location where all raw files are
RAWDATA_DIR = '/home/cmb-06/as/skchoudh/dna/Luiz_radiation_data/Penalva_08242016_Run160902/Penalva_08242016'


## Output directory
OUT_DIR = '/staging/as/skchoudh/rna/Feb_02_2017_Radiation_GBM_ribo'


## Absolute location to 're-ribo/scripts' directory
SRC_DIR = '/auto/cmb-panasas2/skchoudh/github_projects/re-ribo-mine/scripts'


## Genome fasta location
GENOME_FASTA = '/home/cmb-panasas2/skchoudh/genomes/hg38/fasta/hg38.fa'


## Chromosome sizes location
CHROM_SIZES = '/home/cmb-panasas2/skchoudh/genomes/hg38/fasta/hg38.chrom.sizes'



## Path to STAR index (will be generated if does not exist)
STAR_INDEX = '/home/cmb-panasas2/skchoudh/genomes/hg38/star_annotated'


## GTF path
GTF = '/home/cmb-panasas2/skchoudh/genomes/hg38/annotation/gencode.v25.annotation.without_rRNA_tRNA.gtf'


## GenePred bed downloaded from UCSC
## (this is used for inferring the type of experiment i.e stranded/non-stranded
## and hence is not required)
GENE_BED = '/home/cmb-panasas2/skchoudh/genomes/hg38/annotation/gencode.v24.genes.bed'


## Path to bed file with start codon coordinates
START_CODON_BED = '/home/cmb-panasas2/skchoudh/genomes/hg38/annotation/gencode.v25.gffutils.start_codon.bed'


## Path to bed file with stop codon coordinates
STOP_CODON_BED = '/home/cmb-panasas2/skchoudh/genomes/hg38/annotation/gencode.v25.gffutils.stop_codon.bed'


## Path to bed file containing CDS coordinates
CDS_BED = '/home/cmb-panasas2/skchoudh/genomes/hg38/annotation/gencode.v25.gffutils.cds.bed'

# We don't have these so just use CDs bed to get the pipeline running
UTR5_BED = '/home/cmb-panasas2/skchoudh/genomes/hg38/annotation/gencode.v25.gffutils.UTR5.bed'

UTR3_BED = '/home/cmb-panasas2/skchoudh/genomes/hg38/annotation/gencode.v25.gffutils.UTR3.bed'


## Name of python2 environment
## The following package needs to be installed in that environment
## numpy scipy matploltib seaborn pysam pybedtools htseq
## you can do: conda create -n python2 PYTHON=2 && source activate python2 && conda install numpy scipy matploltib seaborn pysam pybedtools htseq

PYTHON2ENV = 'python2'

############################################Do Not Edit#############################################
HTSEQ_STRANDED = 'yes'
FEATURECOUNTS_S = '-s 1'
FEATURECOUNTS_T = 'CDS'
HTSEQ_MODE = 'intersection-strict'

