pbsmrtpipe supports python, R and Scala for via the pacbio Tool Contract interface.
Requires python (2.7.9) with virtualenv
Currently tested with:
Python:
- pbcommand==0.3.27
- pbcore==1.2.10
- pbcoretools==0.1.10
- pbreports==2.5.1
- pbsmrtpipe==0.40.1
R:
- pbcommandR 0.3.3
Installing the necessary python components:
$> virtualenv ve
$> source ve/bin/activate
$> # this will install pbcommand, pbcore and pbsmrtpipe from github repos.
$> # modify the REQUIREMENTS.txt file to point to other versions
$> pip install -r REQUIREMENTS.txt
Note, the REQUIREMENTS.txt file is pulling from master, this might be incompatible with newer versions.
$> # set path to TCs so pbsmrtpipe can load them
$> export PB_TOOL_CONTRACT_DIR=$(pwd)/tool-contracts
$> pbsmrtpipe show-tasks # your tasks should show up in the registry
$> # add *.py examples to our path
$> export PATH=$(pwd):$PATH
$> # Sanity check
$> # rebuild Tool Contracts
$> make py-tool-contracts
$> pbsmrtpipe show-tasks # final check to see if your tasks are in the registry
Or call the included setup-env.sh to setup the python ENV.
$> source setup-env.sh # will set the TC env var and PATH
Install pbcommandR using install_githhub("PacificBiosciences/pbcommandR")
Set the R_LIBS custom path and bin directory for pbcommandR exes.
Example:
$> export R_LIBS=/Users/mkocher/gh_projects/pbcommandR/packrat/lib/x87_64-apple-darwin15.4.0/3.3.0
$> export PATH=/Users/mkocher/gh_projects/pbcommandR/bin:$PATH
$> cd py-examples/01-helloworld
$> # pipeline definition
$> cat pipeline.xml
$> # preset defintion
$> cat preset.xml
$> # test layer
$> cat testkit.cfg
$> # This will call pbsmrtpipe and run a sanity tests
$> pbtestkit-runner testkit.cfg
$> # output will be in job_output
$> cd job_output
Or run make target
$> make clean
$> make test-r
pbcommmand provides a python interface to define tasks that can be consumed in pbsmrtpipe.
QuickStart to Defining a Task (via ToolContract Interface)
import sys
import logging
from pbcommand.models import FileTypes, OutputFileType
from pbcommand.cli import registry_builder, registry_runner
log = logging.getLogger(__name__)
# the 'Driver' exe needs to be your your path
registry = registry_builder("pbsmrtpipe_examples", "hello_world_quick.py ")
def _example_main(input_files, output_files, **kwargs):
# This func should be imported from your python package.
# This is just for test purposes
log.info("Running example main with {i} {o} kw:{k}".format(i=input_files,
o=output_files, k=kwargs))
# write mock output files, otherwise the End-to-End test will fail
xs = output_files if isinstance(output_files, (list, tuple)) else [output_files]
for x in xs:
with open(x, 'w') as writer:
writer.write("Mock data\n")
return 0
@registry("dev_mk_example_txt", "0.2.1", FileTypes.TXT, FileTypes.TXT, nproc=1, options=dict(alpha=1234))
def run_rtc(rtc):
return _example_main(rtc.task.input_files[0], rtc.task.output_files[0], nproc=rtc.task.nproc)
# More tasks can be registered by calling @registry()
if __name__ == '__main__':
sys.exit(registry_runner(registry, sys.argv[1:]))Install requires packrat and pbcommandR.
> library(devtools)
> install_githhub("PacficBiosciences/pbcommandR")Setup the R_LIBS env var and set the PATH to encluded the root pbcommandR + /bin/ dir
$> cd r-examples/01-helloR
$> # pipeline definition
$> cat pipeline.xml
$> # preset defintion
$> cat preset.xml
$> # test layer
$> cat testkit.cfg
$> # This will call pbsmrtpipe and run a sanity tests
$> pbtestkit-runner testkit.cfg
$> # output will be in job_output
Or run make target
$> make test-r