def get_plan(options, project, inSeqFile, outSeqFile):
plan = get_generation_info() + '\n'
if options.wdl:
plan += wdl_workflow_start(options, inSeqFile)
# preprocessing
plan += '\n## Preprocessor\n'
leaves = [outSeqFile.tree.getName(leaf) for leaf in outSeqFile.tree.getLeaves()]
for i in range(0, len(leaves), options.preprocessBatchSize):
pre_batch = leaves[i:i+options.preprocessBatchSize]
if options.wdl:
assert len(pre_batch) == 1
plan += wdl_call_preprocess(options, inSeqFile, outSeqFile, leaves[i])
else:
plan += 'cactus-preprocess {} {} {} --inputNames {} {} {}\n'.format(
get_jobstore(options), options.seqFile, options.outSeqFile, ' '.join(pre_batch),
options.cactusOptions, get_toil_resource_opts(options, 'preprocess'))
if options.preprocessOnly:
# if we're only making preprocess jobs, we can end early
plan += '\n## Cactus\n'
plan += 'cactus {} {} {} {}\n'.format(get_jobstore(options), options.outSeqFile,
options.outHal, options.cactusOptions)
return plan
# shedule up the alignments
schedule = Schedule()
schedule.loadProject(project)
schedule.compute()
# set of all jobs, as genome names from the (fully resolved, output) seqfile
events = set(outSeqFile.pathMap.keys()) - set(leaves)
resolved = set(leaves)
# convert follow-ons to dependencies
follow_on_deps = {}
for event in events:
fo = schedule.followOn(event)
if fo:
follow_on_deps[fo] = event
def get_deps(event):
deps = set(schedule.deps(event))
if event in follow_on_deps:
deps = deps.union(set(follow_on_deps[event]))
# I don't know why the schedule doesn't always give the children
# todo: understand!
try:
has_name = outSeqFile.tree.getNodeId(event) is not None
except:
has_name = False
if has_name:
for node in outSeqFile.tree.getChildren(outSeqFile.tree.getNodeId(event)):
if not outSeqFile.tree.isLeaf(node):
deps.add(outSeqFile.tree.getName(node))
return deps
events_and_virtuals = set()
# there can be chains of virtual events not caught by a single round
# of get_deps, so we iterate till we have them all
to_add = set()
for event in events:
to_add.add(event)
while len(to_add) > 0:
to_add1 = set()
for event in to_add:
events_and_virtuals.add(event)
for dep in get_deps(event):
if dep not in events_and_virtuals and dep not in to_add:
to_add1.add(dep)
to_add = to_add1
# group jobs into rounds. where all jobs of round i can be run in parallel
groups = []
while len(events_and_virtuals) > 0:
group = []
to_remove = []
added = 0
for event in events_and_virtuals:
if all([dep in resolved for dep in get_deps(event)]):
if not schedule.isVirtual(event):
group.append(event)
to_remove.append(event)
added += 1
if added == 0:
sys.stderr.write("schedule deadlock:\n")
for event in events_and_virtuals:
sys.stderr.write("{} has deps {}\n".format(event, ["{}(resolved={})".format(d, d in resolved) for d in get_deps(event)]))
sys.exit(1)
for tr in to_remove:
resolved.add(tr)
events_and_virtuals.remove(tr)
groups.append(group)
def halPath(event):
if event == project.mcTree.getRootName():
return options.outHal
else:
return os.path.join(options.outDir, event + '.hal')
def cigarPath(event):
return os.path.join(options.outDir, event + '.cigar')
# alignment groups
plan += '\n## Alignment\n'
for i, group in enumerate(groups):
plan += '\n### Round {}'.format(i)
for event in sorted(group):
plan += '\n'
if options.wdl:
plan += wdl_call_blast(options, project, event, cigarPath(event))
plan += wdl_call_align(options, project, event, cigarPath(event), halPath(event), outSeqFile.pathMap[event])
else:
# todo: support cactus interface (it's easy enough here, but cactus_progressive.py needs changes to handle)
plan += 'cactus-blast {} {} {} --root {} {} {}\n'.format(
get_jobstore(options), options.outSeqFile, cigarPath(event), event,
options.cactusOptions, get_toil_resource_opts(options, 'blast'))
plan += 'cactus-align {} {} {} {} --root {} {} {}\n'.format(
get_jobstore(options), options.outSeqFile, cigarPath(event), halPath(event), event,
options.cactusOptions, get_toil_resource_opts(options, 'align'))
# todo: just output the fasta in cactus-align.
plan += 'hal2fasta {} {} {} > {}\n'.format(halPath(event), event, options.halOptions, outSeqFile.pathMap[event])
# stitch together the final tree
plan += '\n## HAL merging\n'
root = project.mcTree.getRootName()
prev_event = None
append_count = 0
for group in reversed(groups):
for event in group:
if event != root:
if options.wdl:
plan += wdl_call_hal_append(options, project, event, prev_event)
else:
plan += 'halAppendSubtree {} {} {} {} --merge {}\n'.format(
halPath(root), halPath(event), event, event, options.halOptions)
append_count += 1
prev_event = event
if options.wdl:
plan += wdl_workflow_end(options, prev_event, append_count > 1)
return plan
def get_plan(options, project, inSeqFile, outSeqFile, toil):
plan = get_generation_info() + '\n'
if options.wdl:
plan += wdl_workflow_start(options, inSeqFile)
options.pp_map = {}
if options.toil:
# kick things off with an empty job which we will hook subsequent jobs onto
# (using RoundedJob because root job must be sublcass of Job,
# https://github.com/ComparativeGenomicsToolkit/cactus/pull/284#issuecomment-684125478)
start_job = RoundedJob()
parent_job = start_job
job_idx = {}
# preprocessing
plan += '\n## Preprocessor\n'
leaves = [outSeqFile.tree.getName(leaf) for leaf in outSeqFile.tree.getLeaves()]
for i in range(0, len(leaves), options.preprocessBatchSize):
pre_batch = leaves[i:i+options.preprocessBatchSize]
if options.wdl:
plan += wdl_call_preprocess(options, inSeqFile, outSeqFile, pre_batch)
elif options.toil:
job_idx[("preprocess", leaves[i])] = parent_job.addChildJobFn(toil_call_preprocess, options, inSeqFile, outSeqFile, leaves[i],
cores=options.preprocessCores,
memory=options.preprocessMemory,
disk=options.preprocessDisk)
else:
plan += 'cactus-preprocess {} {} {} --inputNames {} {} {}\n'.format(
get_jobstore(options), options.seqFile, options.outSeqFile, ' '.join(pre_batch),
options.cactusOptions, get_toil_resource_opts(options, 'preprocess'))
if options.preprocessOnly:
plan += '\n## Cactus\n'
plan += 'cactus {} {} {} {}\n'.format(get_jobstore(options), options.outSeqFile,
options.outHal, options.cactusOptions)
return plan
# shedule up the alignments
schedule = Schedule()
schedule.loadProject(project)
schedule.compute()
# set of all jobs, as genome names from the (fully resolved, output) seqfile
events = set(outSeqFile.pathMap.keys()) - set(leaves)
resolved = set(leaves)
# convert follow-ons to dependencies
follow_on_deps = {}
for event in events:
fo = schedule.followOn(event)
if fo:
follow_on_deps[fo] = event
def get_deps(event):
deps = set(schedule.deps(event))
if event in follow_on_deps:
deps = deps.union(set(follow_on_deps[event]))
# I don't know why the schedule doesn't always give the children
# todo: understand!
try:
has_name = outSeqFile.tree.getNodeId(event) is not None
except:
has_name = False
if has_name:
for node in outSeqFile.tree.getChildren(outSeqFile.tree.getNodeId(event)):
if not outSeqFile.tree.isLeaf(node):
deps.add(outSeqFile.tree.getName(node))
return deps
events_and_virtuals = set(events)
# add all events, potentially looping through virtual dependency chains
# (hence the double loop)
batch = set(events_and_virtuals)
while len(batch) > 0:
next_batch = set()
for event in batch:
for dep in get_deps(event):
if dep not in events_and_virtuals:
next_batch.add(dep)
events_and_virtuals.add(dep)
batch = next_batch
# group jobs into rounds. where all jobs of round i can be run in parallel
groups = []
while len(events_and_virtuals) > 0:
group = []
to_remove = []
added = 0
for event in events_and_virtuals:
if all([dep in resolved for dep in get_deps(event)]):
if not schedule.isVirtual(event):
group.append(event)
to_remove.append(event)
added += 1
if added == 0:
sys.stderr.write("schedule deadlock:\n")
for event in events_and_virtuals:
sys.stderr.write("{} has deps {}\n".format(event, get_deps(event)))
sys.exit(1)
for tr in to_remove:
resolved.add(tr)
events_and_virtuals.remove(tr)
groups.append(group)
def halPath(event):
if event == project.mcTree.getRootName():
return options.outHal
else:
return os.path.join(options.outDir, event + '.hal')
def cigarPath(event):
return os.path.join(options.outDir, event + '.cigar')
# alignment groups
plan += '\n## Alignment\n'
for i, group in enumerate(groups):
plan += '\n### Round {}'.format(i)
if options.toil:
# advance toil phase
# todo: recapitulate exact dependencies
parent_job = parent_job.addFollowOn(Job())
for event in sorted(group):
plan += '\n'
if options.wdl:
plan += wdl_call_blast(options, project, event, cigarPath(event))
plan += wdl_call_align(options, project, event, cigarPath(event), halPath(event), outSeqFile.pathMap[event])
elif options.toil:
# promises only get fulfilleed if they are passed directly as arguments to the toil job, so we pull out the ones we need here
leaf_deps, anc_deps = get_dep_names(options, project, event)
fa_promises = [job_idx[("preprocess", dep)].rv() for dep in leaf_deps] + [job_idx[("align", dep)].rv(0) for dep in anc_deps]
job_idx[("blast", event)] = parent_job.addChildJobFn(toil_call_blast,
options,
outSeqFile,
project,
event,
cigarPath(event),
leaf_deps + anc_deps,
*fa_promises,
cores=options.blastCores,
memory=options.blastMemory,
disk=options.preprocessDisk)
job_idx[("align", event)] = job_idx[("blast", event)].addFollowOnJobFn(toil_call_align,
options, outSeqFile,
project,
event,
cigarPath(event),
halPath(event),
outSeqFile.pathMap[event],
job_idx[("blast", event)].rv(),
leaf_deps + anc_deps, *fa_promises,
cores=options.alignCores,
memory=options.alignMemory,
disk=options.alignDisk)
else:
# todo: support cactus interface (it's easy enough here, but cactus_progressive.py needs changes to handle)
plan += 'cactus-blast {} {} {} --root {} {} {}\n'.format(
get_jobstore(options), options.outSeqFile, cigarPath(event), event,
options.cactusOptions, get_toil_resource_opts(options, 'blast'))
plan += 'cactus-align {} {} {} {} --root {} {} {} --database {}\n'.format(
get_jobstore(options), options.outSeqFile, cigarPath(event), halPath(event), event,
options.cactusOptions, get_toil_resource_opts(options, 'align'), options.database)
# todo: just output the fasta in cactus-align.
plan += 'hal2fasta {} {} {} > {}\n'.format(halPath(event), event, options.halOptions, outSeqFile.pathMap[event])
# advance toil phase
if options.toil:
parent_job = parent_job.addFollowOn(Job())
# stitch together the final tree
plan += '\n## HAL merging\n'
root = project.mcTree.getRootName()
prev_event = None
append_count = 0
event_list = []
for group in reversed(groups):
for event in group:
if event != root:
if options.wdl:
plan += wdl_call_hal_append(options, project, event, prev_event)
elif not options.toil:
plan += 'halAppendSubtree {} {} {} {} --merge {}\n'.format(
halPath(root), halPath(event), event, event, options.halOptions)
append_count += 1
event_list.append(event)
prev_event = event
if options.toil:
job_idx['hal_append'] = parent_job.addChildJobFn(toil_call_hal_append_subtrees,
options,
project,
root,
job_idx[('align', root)].rv(1),
event_list,
*[job_idx[('align', e)].rv(1) for e in event_list],
cores=1,
memory=options.alignMemory,
disk=options.halAppendDisk)
if options.wdl:
plan += wdl_workflow_end(options, prev_event, append_count > 1)
if options.toil:
start_time = timeit.default_timer()
toil.start(start_job)
end_time = timeit.default_timer()
run_time = end_time - start_time
logger.info("cactus-prepare-toil has finished after {} seconds".format(run_time))
return plan