def main(order):
piper = PiperFactory.create_piper(order)
play_pipe(piper)
def play_pipe(piper):
piper.pipe_stdin()
cmd = piper.render_user_cmd(order=piper.order,)
piper.run_user_script(cmd)
piper.collect_output_files()
piper.upload_output_files()
piper.teardown()
├── seqpiper
│ ├── base
│ ├── bam
│ ├── vcf
│ │ ├── base.py
│ │
│ ├── main.py
│
├── tests
├── phasing.sh
├── imputation.sh
class VcfPiperBase(PiperAbstractFactory):
def pipe_stdin(self):
some_vcf_function()
class PiperAbstractFactory(object):
@abstractmethod
def stdin(self):
pass
def render_user_cmd(self):
some code
def run_user_script(self):
some code
def collect_output_files(self):
some code
def upload_output_files(self):
some code
def teardown(self):
some code
import sys
import traceback
sys.path.append('/usr/local/seqslab/SeqPiper')
from script.library.GatkWrapper import ApplyRecalibration
from script.common.base import SeqPiperBase
from script.common.order import JobOrder
from script.common.exception import SeqPiperEmptyVariantFile
import sys
import traceback
from script.library.GatkWrapper import ApplyRecalibration
from script.common.base import SeqPiperBase
from script.common.order import JobOrder
from script.common.exception import SeqPiperEmptyVariantFile
sys.path.append('/usr/local/seqslab/SeqPiper')
setup(
name="seqpiper",
version="0.0.1",
long_description=readme,
long_description_content_type="text/markdown",
url="",
author="",
author_email="",
license="",
install_requires=[],
keywords="bioinformatics, seqpiper",
packages=find_packages(),
)
python3 setup.py install
import sys
import traceback
from script.library.GatkWrapper import ApplyRecalibration
from script.common.base import SeqPiperBase
from script.common.order import JobOrder
from script.common.exception import SeqPiperEmptyVariantFile
/opt/bitnami/spark/bin/spark-submit \
--class net.vartotal.piper.cli.PiperMain \
--driver-cores 1 \
--driver-memory 1g \
--executor-cores 1 \
--executor-memory 10g \
--conf "spark.dynamicAllocation.enabled=false" \
--conf "spark.executor.extraJavaOptions=-XX:+UseG1GC" \
--conf "spark.serializer=org.apache.spark.serializer.KryoSerializer" \
--conf "spark.kryo.registrator=net.vartotal.piper.serialization.ADAMKryoRegistrator" \
--conf "spark.executor.memoryOverhead=14g" \
--conf "spark.speculation=false" \
/usr/local/seqslab/SeqPiper/target/piper-2.1.0.jar vcf \
--reference-version 38 \
--reference-system GRCH \
--piper-script fixtures.scripts.no_stdout \
-i 0=/usr/local/seqslab/SeqPiper/fixtures/vcf/ \
--samplePath /usr/local/seqslab/SeqPiper/fixtures/vcf/ \
--vcf-output-path vcf_gz_folder \
--partition-bed-path /usr/local/seqslab/SeqPiper/fixtures/bed/38/chromosomes
├── seqpiper
│ ├── base
│ ├── bam
│ ├── vcf
│ │ ├── base.py
│ │
│ ├── main.py
│
├── tests
├── phasing.sh
├── imputation.sh