Installing and Hello World

Release versions are posted on the GitHub releases page. You can install the latest version directly from GitHub using pip:

pip install --user

Update with:

pip install --user --upgrade

Now, to test pypiper, follow the commands in the Hello, Pypiper! tutorial: just run these 3 lines of code and you’re running your first pypiper pipeline!

# Install the latest version of pypiper:
pip install --user

# download

# Run it:

The actual code, in is a very simple but complete pipeline:

#!/usr/bin/env python

import pypiper
outfolder = "hello_pypiper_results" # Choose a folder for your results
pm = pypiper.PipelineManager(name="hello_pypiper", outfolder=outfolder)

target_file = "hello_pypiper_results/output.txt"
cmd = "echo 'Hello, Pypiper!' > " + target_file, target_file)


When you run it, you should see printed to screen some output like this:

##### [Pipeline run code and environment:]
*              Command:  ``
*         Compute host:  puma
*          Working dir:  /home/nsheff
*            Outfolder:  hello_pypiper_results/
*  Pipeline started at:   (08-24 12:34:34) elapsed:0:00:00 _TIME_

##### [Version log:]
*       Python version:  2.7.12
*          Pypiper dir:  `/home/nsheff/.local/lib/python2.7/site-packages/pypiper`
*      Pypiper version:  0.6.0
*         Pipeline dir:  `/home/nsheff`
*     Pipeline version:  None

##### [Arguments passed to pipeline:]


Change status from initializing to running
Hello! (08-24 12:34:34) elapsed:0:00:00 _TIME_

Target to produce: `hello_pypiper_results/output.txt`
> `echo 'Hello, Pypiper!' > hello_pypiper_results/output.txt`

Process 2325 returned: (0). Elapsed: 0:00:00.

Change status from running to completed
> `Time`        0:00:00 hello_pypiper   _RES_
> `Success`     08-24-12:34:34  hello_pypiper   _RES_

##### [Epilogue:]
*   Total elapsed time:  0:00:00
*     Peak memory used:  0.0 GB
* Pipeline completed at:  (08-24 12:34:34) elapsed:0:00:00 _TIME_

Pypiper terminating spawned child process 2318...
child process terminated

This output is printed to your screen and also recorded in a log file (called There are a few other outputs from the pipeline as well. All results are placed in a folder called hello_pypiper_results. Navigate to that folder to observe the output of the pipeline, which will include these files:

  • hello_pypiper_completed.flag
  • hello_pypiper_profile.tsv
  • output.txt
  • stats.tsv

These files are explained in more detail in the next section, so head right on over to outputs explained or to the features list. If you’re ready, you can also just dive right in with some more in-depth tutorials.