cre.bcbio.custom_genome.sh

#!/bin/bash

# crashes on qlogin node, building indexes takes time

#PBS -l walltime=48:00:00,nodes=1:ppn=20
#PBS -joe .
#PBS -d .
#PBS -l vmem=50g,mem=50g

hostname
echo $PATH
echo $PYTHONPATH

#wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz

gunzip hs37d5.fa.gz

bcbio_setup_genome.py -f hs37d5.fa -g /hpf/largeprojects/ccmbio/naumenko/tools/bcbio_1.1.5/genomes/Hsapiens/GRCh37/rnaseq/ref-transcripts.gtf -n Hsapiens -b GRCh37d5 -i bwa star rtg -c 20