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#!/usr/bin/env python
"""Getting Started: A simple sample pipeline built using pypiper."""
# This is a runnable example. You can run it to see what the output
# looks like.
# First, make sure you can import the pypiper package
import os
import pypiper
# Create a PipelineManager instance (don't forget to name it!)
# This starts the pipeline.
pm = pypiper.PipelineManager(name="BASIC",
outfolder="pipeline_output/")
# Now just build shell command strings, and use the run function
# to execute them in order. run needs 2 things: a command, and the
# target file you are creating.
# First, generate some random data
# specify target file:
tgt = "pipeline_output/test.out"
# build the command
cmd = "shuf -i 1-500000000 -n 10000000 > " + tgt
# and run with run().
pm.run(cmd, target=tgt)
# Now copy the data into a new file.
# first specify target file and build command:
tgt = "pipeline_output/copied.out"
cmd = "cp pipeline_output/test.out " + tgt
pm.run(cmd, target=tgt)
# You can also string multiple commands together, which will execute
# in order as a group to create the final target.
cmd1 = "sleep 5"
cmd2 = "touch pipeline_output/touched.out"
pm.run([cmd1, cmd2], target="pipeline_output/touched.out")
# A command without a target will run every time.
# Find the biggest line
cmd = "awk 'n < $0 {n=$0} END{print n}' pipeline_output/test.out"
pm.run(cmd, "lock.max")
# Use checkprint() to get the results of a command, and then use
# report_result() to print and log key-value pairs in the stats file:
last_entry = pm.checkprint("tail -n 1 pipeline_output/copied.out")
pm.report_result("last_entry", last_entry)
# Now, stop the pipeline to complete gracefully.
pm.stop_pipeline()
# Observe your outputs in the pipeline_output folder
# to see what you've created.
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