def test_mpi_builder__multithreaded__complex_cmd():
builder = AtomicMPICmdBuilder(["python", "/foo/run.py"], threads=3)
assert_equal(builder.call, ["mpirun", "-n", 3, "python", "/foo/run.py"])
assert_equal(builder.kwargs, {"EXEC_MAIN": "python"})
def test_mpi_builder__kwargs():
builder = AtomicMPICmdBuilder("ls", set_cwd=True)
assert_equal(builder.kwargs, {"set_cwd": True, "EXEC_MPI": "mpirun"})
def test_mpi_builder__defaults__complex_cmd():
builder = AtomicMPICmdBuilder(["python", "/foo/run.py"])
assert_equal(builder.call, ["python", "/foo/run.py"])
assert_equal(builder.kwargs, {"EXEC_MPI": "mpirun"})
def test_mpi_builder__multithreaded__str():
builder = AtomicMPICmdBuilder("ls", threads=3)
assert_equal(builder.call, ["mpirun", "-n", 3, "ls"])
assert_equal(builder.kwargs, {"EXEC_MAIN": "ls"})
def test_mpi_builder__defaults__str():
builder = AtomicMPICmdBuilder("ls")
assert_equal(builder.call, ["ls"])
assert_equal(builder.kwargs, {"EXEC_MPI": "mpirun"})
def customize(cls, input_binary, initial_tree, output_template, threads = 1, dependencies = ()):
"""
Arguments:
input_binary -- A binary alignment file in a format readable by ExaML.
output_template -- A template string used to construct final filenames. Should consist
of a full path, including a single '%s', which is replaced with the
variable part of RAxML output files (e.g. 'info', 'bestTree', ...).
Example destination: '/disk/project/SN013420.RAxML.%s'
Example output: '/disk/project/SN013420.RAxML.bestTree'"""
# TODO: Make MPIParams!
command = AtomicMPICmdBuilder("examl", threads = threads)
# Ensures that output is saved to the temporary directory
command.set_option("-w", "%(TEMP_DIR)s")
command.set_option("-s", "%(IN_ALN)s")
command.set_option("-t", "%(IN_TREE)s")
command.set_option("-n", "Pypeline")
command.set_kwargs(IN_ALN = input_binary,
IN_TREE = initial_tree,
# Final output files, are not created directly
OUT_INFO = output_template % "info",
OUT_BESTTREE = output_template % "result",
OUT_BOOTSTRAP = output_template % "log",
CHECK_EXAML = EXAML_VERSION)
# Use the GAMMA model of NT substitution by default
command.set_option("-m", "GAMMA", fixed = False)
return {"command" : command}
def customize(cls,
input_binary,
initial_tree,
output_template,
threads=1,
dependencies=()):
"""
Arguments:
input_binary -- A binary alignment file in a format readable by EXaML.
output_template -- A template string used to construct final filenames. Should consist
of a full path, including a single '%s', which is replaced with the
variable part of RAxML output files (e.g. 'info', 'bestTree', ...).
Example destination: '/disk/project/SN013420.RAxML.%s'
Example output: '/disk/project/SN013420.RAxML.bestTree'"""
# TODO: Make MPIParams!
command = AtomicMPICmdBuilder("examl", threads=threads)
# Ensures that output is saved to the temporary directory
command.set_option("-w", "%(TEMP_DIR)s")
command.set_option("-s", "%(IN_ALN)s")
command.set_option("-t", "%(IN_TREE)s")
command.set_option("-n", "Pypeline")
command.set_kwargs(
IN_ALN=input_binary,
IN_TREE=initial_tree,
# Final output files, are not created directly
OUT_INFO=output_template % "info",
OUT_BESTTREE=output_template % "result",
OUT_BOOTSTRAP=output_template % "log")
# Use the GAMMA model of NT substitution by default
command.set_option("-m", "GAMMA", fixed=False)
return {"command": command}