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BWA_VERSION=bwa-0.7.17
all: bwa work_queue_server work_queue_server.py ref.fastq.ann query.fastq.0.gz
work_queue_server:
ln -s ../../work_queue/src/work_queue_server .
work_queue_server.py:
ln -s ../../work_queue/src/clients/python3/work_queue_server.py .
bwa: ${BWA_VERSION}
cd ${BWA_VERSION} && make && cd .. && cp ${BWA_VERSION}/bwa .
${BWA_VERSION}:
curl -L https://sourceforge.net/projects/bio-bwa/files/${BWA_VERSION}.tar.bz2/download > ${BWA_VERSION}.tar.bz2
bunzip2 ${BWA_VERSION}.tar.bz2
tar xvf ${BWA_VERSION}.tar
ref.fastq: fastq_generate.pl
./fastq_generate.pl 100000 1000 > ref.fastq
query.fastq: fastq_generate.pl
./fastq_generate.pl 10000000 10 > query.fastq #5 splits
ref.fastq.ann: ref.fastq bwa
./bwa index ref.fastq
query.fastq.0: query.fastq create_splits.py
./create_splits.py
query.fastq.0.gz: query.fastq.0
gzip -f query.fastq.*
clean:
rm -rf query.fastq.0.* ref.fastq ref.fastq.* query.fastq ${BWA_VERSION} ${BWA_VERSION}.* bwa work_queue_server.py work_queue_server *.pyc
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