setup_test.sh

PROJECT_DIR=$(pwd)/test

mkdir -p ${PROJECT_DIR}/genome
cd ${PROJECT_DIR}/genome
wget --no-check-certificate http://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/sacCer3.chrom.sizes
wget --no-check-certificate http://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/chromFa.tar.gz
{ tar -O -xf chromFa.tar.gz && rm chromFa.tar.gz; } | gzip -c > sacCer3.fa.gz
# bwa index sacCer3.fa.gz

mkdir -p ${PROJECT_DIR}/fastq/MATalpha_R1/lane1/
mkdir -p ${PROJECT_DIR}/fastq/MATalpha_R1/lane2/
mkdir -p ${PROJECT_DIR}/fastq/MATalpha_R2/lane1/
mkdir -p ${PROJECT_DIR}/fastq/MATa_R1/lane1/
mkdir -p ${PROJECT_DIR}/fastq/MATa_R2/lane1/

cd ${PROJECT_DIR}/fastq/MATalpha_R1/lane1/
fastq-dump -F -X 100000 SRR2601842 --split-files --gzip
#cd ${PROJECT_DIR}/fastq/MATalpha_R1/lane2/
#fastq-dump -F -X 100000 SRR2601843 --split-files --gzip
cd ${PROJECT_DIR}/fastq/MATalpha_R2/lane1/
fastq-dump -F -X 100000 SRR2601845 --split-files --gzip
cd ${PROJECT_DIR}/fastq/MATa_R1/lane1/
fastq-dump -F -X 100000 SRR2601848 --split-files --gzip
cd ${PROJECT_DIR}/fastq/MATa_R2/lane1/
fastq-dump -F -X 100000 SRR2601851 --split-files --gzip