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daxgen.py
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daxgen.py
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#!/usr/bin/env python
import sys
import string
import os
from datetime import datetime
from ConfigParser import ConfigParser
from Pegasus.DAX3 import ADAG, Job, File, Link
DAXGEN_DIR = os.path.dirname(os.path.realpath(__file__))
class MGRASTWorkflow(object):
def __init__(self, outdir, config, mgfile):
"'outdir' is the directory where the workflow is written, and 'config' is a ConfigParser object"
self.outdir = outdir
self.config = config
self.mgfile = mgfile
self.daxfile = os.path.join(self.outdir, "dax.xml")
self.replicas = {}
# Get all the values from the config file
self.file_format = config.get("simulation", "file_format")
self.assembled = config.get("simulation", "assembled")
self.filter_options = config.get("simulation", "filter_options")
self.prefix_length = config.get("simulation", "prefix_length")
self.dereplicate = config.get("simulation", "dereplicate")
self.m5rna_clust = config.get("simulation", "m5rna_clust")
self.screen_indexes = config.get("simulation", "screen_indexes")
self.bowtie = config.get("simulation", "bowtie")
self.fgs_type = config.get("simulation", "fgs_type")
self.aa_pid = config.get("simulation", "aa_pid")
self.ach_annotation_ver = config.get("simulation", "ach_annotation_ver")
self.rna_pid = config.get("simulation", "rna_pid")
def add_replica(self, name, path):
"Add a replica entry to the replica catalog for the workflow"
url = path
if url is None:
url = "gsiftp://${SITE_URL}/${MGRAST_DIR}/predata/%s" % name
self.replicas[name] = url
def generate_replica_catalog(self):
"Write the replica catalog for this workflow to a file"
path = os.path.join(self.outdir, "rc.template")
f = open(path, "w")
try:
pool = "local"
for name, url in self.replicas.items():
if not url.startswith("gsiftp://"):
url = "file://%s" % url
f.write('%-30s %-100s pool="%s"\n' % (name, url, pool))
finally:
f.close()
def generate_workflow(self):
"Generate a workflow (DAX, config files, and replica catalog)"
ts = datetime.utcnow().strftime('%Y%m%dT%H%M%SZ')
dax = ADAG("mgrast-prod-%s" % ts)
# These are all the global input files for the workflow
metagenome = File(self.mgfile)
self.add_replica(self.mgfile, os.path.abspath(self.mgfile))
# QC job
qcJob = Job("wrapper-qc", node_label="wrapper-qc")
qcJob.addArguments("-input", self.mgfile)
qcJob.addArguments("-format", self.file_format)
qcJob.addArguments("-out_prefix", "075")
qcJob.addArguments("-assembled", self.assembled)
qcJob.addArguments("-filter_options", self.filter_options)
qcJob.addArguments("-proc", "8")
qcJob.uses(metagenome, link=Link.INPUT)
qcJob.uses("075.assembly.coverage", link=Link.OUTPUT, transfer=False)
qcJob.uses("075.qc.stats", link=Link.OUTPUT, transfer=False)
qcJob.uses("075.upload.stats", link=Link.OUTPUT, transfer=False)
qcJob.profile("globus", "maxwalltime", "60")
qcJob.profile("globus", "hostcount", "8")
qcJob.profile("globus", "count", "8")
dax.addJob(qcJob)
# Preprocess Job
preprocessJob = Job("wrapper-preprocess", node_label="wrapper-preprocess")
preprocessJob.addArguments("-input", self.mgfile)
preprocessJob.addArguments("-format", self.file_format)
preprocessJob.addArguments("-out_prefix", "100.preprocess")
preprocessJob.addArguments("-filter_options", self.filter_options)
preprocessJob.uses(metagenome, link=Link.INPUT)
preprocessJob.uses("100.preprocess.passed.fna", link=Link.OUTPUT, transfer=False)
preprocessJob.uses("100.preprocess.removed.fna", link=Link.OUTPUT, transfer=False)
preprocessJob.profile("globus", "maxwalltime", "20")
dax.addJob(preprocessJob)
# Dereplicate Job
dereplicateJob = Job("wrapper-dereplicate", node_label="wrapper-dereplicate")
dereplicateJob.addArguments("-input=100.preprocess.passed.fna")
dereplicateJob.addArguments("-out_prefix=150.dereplication")
dereplicateJob.addArguments("-prefix_length=%s" % self.prefix_length)
dereplicateJob.addArguments("-dereplicate=%s" % self.dereplicate)
dereplicateJob.addArguments("-memory=10")
dereplicateJob.uses("100.preprocess.passed.fna", link=Link.INPUT)
dereplicateJob.uses("150.dereplication.passed.fna", link=Link.OUTPUT, transfer=False)
dereplicateJob.uses("150.dereplication.removed.fna", link=Link.OUTPUT, transfer=False)
dereplicateJob.profile("globus", "maxwalltime", "10")
dax.addJob(dereplicateJob)
dax.depends(dereplicateJob, preprocessJob)
# Bowtie Screen Job
bowtieJob = Job("wrapper-bowtie-screen", node_label="wrapper-bowtie-screen")
bowtieJob.addArguments("-input=150.dereplication.passed.fna")
bowtieJob.addArguments("-output=299.screen.passed.fna")
bowtieJob.addArguments("-index=%s" % self.screen_indexes)
bowtieJob.addArguments("-bowtie=%s" % self.bowtie)
bowtieJob.addArguments("-proc=8")
bowtieJob.uses("150.dereplication.passed.fna", link=Link.INPUT)
bowtieJob.uses("299.screen.passed.fna", link=Link.OUTPUT, transfer=False)
bowtieJob.profile("globus", "maxwalltime", "30")
bowtieJob.profile("globus", "hostcount", "8")
bowtieJob.profile("globus", "count", "8")
dax.addJob(bowtieJob)
dax.depends(bowtieJob, dereplicateJob)
# Genecalling Job
geneJob = Job("wrapper-genecalling", node_label="wrapper-genecalling")
geneJob.addArguments("-input=299.screen.passed.fna")
geneJob.addArguments("-out_prefix=350.genecalling.coding")
geneJob.addArguments("-type=%s" % self.fgs_type)
geneJob.addArguments("-size=100")
geneJob.addArguments("-proc=8")
geneJob.uses("299.screen.passed.fna", link=Link.INPUT)
geneJob.uses("350.genecalling.coding.faa", link=Link.OUTPUT, transfer=False)
geneJob.uses("350.genecalling.coding.fna", link=Link.OUTPUT, transfer=False)
geneJob.profile("globus", "maxwalltime", "30")
geneJob.profile("globus", "hostcount", "8")
geneJob.profile("globus", "count", "8")
dax.addJob(geneJob)
dax.depends(geneJob, bowtieJob)
# Cluster (Genecalling) Job
cluster1Job = Job("wrapper-cluster", node_label="wrapper-cluster")
cluster1Job.addArguments("-input=350.genecalling.coding.faa")
cluster1Job.addArguments("-out_prefix=550.cluster")
cluster1Job.addArguments("-aa")
cluster1Job.addArguments("-pid=%s" % self.aa_pid)
cluster1Job.addArguments("-memory=20")
cluster1Job.uses("350.genecalling.coding.faa", link=Link.INPUT)
cluster1Job.uses("550.cluster.aa%s.faa" % self.aa_pid, link=Link.OUTPUT, transfer=False)
cluster1Job.uses("550.cluster.aa%s.mapping" % self.aa_pid, link=Link.OUTPUT, transfer=False)
cluster1Job.profile("globus", "maxwalltime", "10")
dax.addJob(cluster1Job)
dax.depends(cluster1Job, geneJob)
# Blat_prot Job
blatprotJob = Job("wrapper-blat-prot", node_label="wrapper-blat-prot")
blatprotJob.addArguments("--input=550.cluster.aa%s.faa" % self.aa_pid)
blatprotJob.addArguments("--output=650.superblat.sims")
blatprotJob.uses("550.cluster.aa%s.faa" % self.aa_pid, link=Link.INPUT)
blatprotJob.uses("650.superblat.sims", link=Link.OUTPUT, transfer=False)
blatprotJob.profile("globus", "maxwalltime", "2880")
blatprotJob.profile("globus", "hostcount", "24")
blatprotJob.profile("globus", "count", "24")
dax.addJob(blatprotJob)
dax.depends(blatprotJob, cluster1Job)
# Annotate Sims (Blat Prod) Job
annotatesims1Job = Job("wrapper-annotate-sims", node_label="wrapper-annotate-sims")
annotatesims1Job.addArguments("-input=650.superblat.sims")
annotatesims1Job.addArguments("-out_prefix=650")
annotatesims1Job.addArguments("-aa")
annotatesims1Job.addArguments("-ach_ver=%s" % self.ach_annotation_ver)
annotatesims1Job.addArguments("-ann_file=m5nr_v1.bdb")
annotatesims1Job.uses("650.superblat.sims", link=Link.INPUT)
annotatesims1Job.uses("650.aa.sims.filter", link=Link.OUTPUT, transfer=False)
annotatesims1Job.uses("650.aa.expand.protein", link=Link.OUTPUT, transfer=False)
annotatesims1Job.uses("650.aa.expand.lca", link=Link.OUTPUT, transfer=False)
annotatesims1Job.uses("650.aa.expand.ontology", link=Link.OUTPUT, transfer=False)
annotatesims1Job.profile("globus", "maxwalltime", "720")
dax.addJob(annotatesims1Job)
dax.depends(annotatesims1Job, blatprotJob)
# Search RNA Job
searchJob = Job("wrapper-search-rna", node_label="wrapper-search-rna")
searchJob.addArguments("-input=100.preprocess.passed.fna")
searchJob.addArguments("-output=425.search.rna.fna")
searchJob.addArguments("-rna_nr=%s" % self.m5rna_clust)
searchJob.addArguments("-size=100")
searchJob.addArguments("-proc=8")
searchJob.uses("100.preprocess.passed.fna", link=Link.INPUT)
searchJob.uses("425.search.rna.fna", link=Link.OUTPUT, transfer=False)
searchJob.profile("globus", "maxwalltime", "120")
searchJob.profile("globus", "hostcount", "8")
searchJob.profile("globus", "count", "8")
dax.addJob(searchJob)
dax.depends(searchJob, preprocessJob)
# CLuster (Search RNA) Job
cluster2Job = Job("wrapper-cluster", node_label="wrapper-cluster")
cluster2Job.addArguments("-input=425.search.rna.fna")
cluster2Job.addArguments("-out_prefix=440.cluster")
cluster2Job.addArguments("-rna")
cluster2Job.addArguments("-pid=%s" % self.rna_pid)
cluster2Job.addArguments("-memory=20")
cluster2Job.uses("425.search.rna.fna", link=Link.INPUT)
cluster2Job.uses("440.cluster.rna%s.fna" % self.rna_pid, link=Link.OUTPUT, transfer=False)
cluster2Job.uses("440.cluster.rna%s.mapping" % self.rna_pid, link=Link.OUTPUT, transfer=False)
cluster2Job.profile("globus", "maxwalltime", "30")
dax.addJob(cluster2Job)
dax.depends(cluster2Job, searchJob)
# Blat_rna Job
blatrnaJob = Job("wrapper-blat-rna", node_label="wrapper-blat-rna")
blatrnaJob.addArguments("--input=440.cluster.rna%s.fna" % self.rna_pid)
blatrnaJob.addArguments("-rna_nr=m5rna")
blatrnaJob.addArguments("--output=450.rna.sims")
blatrnaJob.addArguments("-assembled=%s" % self.assembled)
blatrnaJob.uses("440.cluster.rna%s.fna" % self.rna_pid, link=Link.INPUT)
blatrnaJob.uses("450.rna.sims", link=Link.OUTPUT, transfer=False)
blatrnaJob.profile("globus", "maxwalltime", "20")
dax.addJob(blatrnaJob)
dax.depends(blatrnaJob, cluster2Job)
# Annotate Sims (Blat RNA) Job
annotatesims2Job = Job("wrapper-annotate-sims", node_label="wrapper-annotate-sims")
annotatesims2Job.addArguments("-input=450.rna.sims")
annotatesims2Job.addArguments("-out_prefix=450")
annotatesims2Job.addArguments("-rna")
annotatesims2Job.addArguments("-ach_ver=%s" % self.ach_annotation_ver)
annotatesims2Job.addArguments("-ann_file=m5nr_v1.bdb")
annotatesims2Job.uses("450.rna.sims", link=Link.INPUT)
annotatesims2Job.uses("450.rna.sims.filter", link=Link.OUTPUT, transfer=False)
annotatesims2Job.uses("450.rna.expand.rna", link=Link.OUTPUT, transfer=False)
annotatesims2Job.uses("450.rna.expand.lca", link=Link.OUTPUT, transfer=False)
annotatesims2Job.profile("globus", "maxwalltime", "30")
dax.addJob(annotatesims2Job)
dax.depends(annotatesims2Job, blatrnaJob)
# Index Sim Seq Job
indexJob = Job("wrapper-index", node_label="wrapper-index")
indexJob.addArguments("-in_seqs=350.genecalling.coding.fna")
indexJob.addArguments("-in_seqs=425.search.rna.fna")
indexJob.addArguments("-in_maps=550.cluster.aa%s.mapping" % self.aa_pid)
indexJob.addArguments("-in_maps=440.cluster.rna%s.mapping" % self.rna_pid)
indexJob.addArguments("-in_sims=650.aa.sims.filter")
indexJob.addArguments("-in_sims=450.rna.sims.filter")
indexJob.addArguments("-output=700.annotation.sims.filter.seq")
indexJob.addArguments("-ach_ver=%s" % self.ach_annotation_ver)
indexJob.addArguments("-memory=10")
indexJob.addArguments("-ann_file=m5nr_v1.bdb")
indexJob.uses("350.genecalling.coding.fna", link=Link.INPUT)
indexJob.uses("550.cluster.aa%s.mapping" % self.aa_pid, link=Link.INPUT)
indexJob.uses("650.aa.sims.filter", link=Link.INPUT)
indexJob.uses("425.search.rna.fna", link=Link.INPUT)
indexJob.uses("440.cluster.rna%s.mapping" % self.rna_pid, link=Link.INPUT)
indexJob.uses("450.rna.sims.filter", link=Link.INPUT)
indexJob.uses("700.annotation.sims.filter.seq", link=Link.OUTPUT, transfer=False)
indexJob.uses("700.annotation.sims.filter.seq.index", link=Link.OUTPUT, transfer=False)
indexJob.profile("globus", "maxwalltime", "120")
dax.addJob(indexJob)
dax.depends(indexJob, geneJob)
dax.depends(indexJob, cluster1Job)
dax.depends(indexJob, cluster2Job)
dax.depends(indexJob, searchJob)
dax.depends(indexJob, annotatesims1Job)
# Annotate Summary Job (13)
summary13Job = Job("wrapper-summary", node_label="wrapper-summary")
summary13Job.addArguments("-job=1")
summary13Job.addArguments("-in_expand=650.aa.expand.protein")
summary13Job.addArguments("-in_expand=450.rna.expand.rna")
summary13Job.addArguments("-in_maps=550.cluster.aa%s.mapping" % self.aa_pid)
summary13Job.addArguments("-in_maps=440.cluster.rna%s.mapping" % self.rna_pid)
summary13Job.addArguments("-in_assemb=075.assembly.coverage")
summary13Job.addArguments("-in_index=700.annotation.sims.filter.seq.index")
summary13Job.addArguments("-output=700.annotation.md5.summary")
summary13Job.addArguments("-nr_ver=%s" % self.ach_annotation_ver)
summary13Job.addArguments("-type=md5")
summary13Job.uses("075.assembly.coverage", link=Link.INPUT)
summary13Job.uses("550.cluster.aa%s.mapping" % self.aa_pid, link=Link.INPUT)
summary13Job.uses("650.aa.expand.protein", link=Link.INPUT)
summary13Job.uses("440.cluster.rna%s.mapping" % self.rna_pid, link=Link.INPUT)
summary13Job.uses("450.rna.expand.rna", link=Link.INPUT)
summary13Job.uses("700.annotation.sims.filter.seq.index", link=Link.INPUT)
summary13Job.uses("700.annotation.md5.summary", link=Link.OUTPUT, transfer=True)
summary13Job.profile("globus", "maxwalltime", "30")
dax.addJob(summary13Job)
dax.depends(summary13Job, qcJob)
dax.depends(summary13Job, cluster1Job)
dax.depends(summary13Job, cluster2Job)
dax.depends(summary13Job, indexJob)
dax.depends(summary13Job, annotatesims1Job)
dax.depends(summary13Job, annotatesims2Job)
# Annotate Summary Job (14)
summary14Job = Job("wrapper-summary", node_label="wrapper-summary")
summary14Job.addArguments("-job=1")
summary14Job.addArguments("-in_expand=650.aa.expand.protein")
summary14Job.addArguments("-in_expand=450.rna.expand.rna")
summary14Job.addArguments("-in_maps=550.cluster.aa%s.mapping" % self.aa_pid)
summary14Job.addArguments("-in_maps=440.cluster.rna%s.mapping" % self.rna_pid)
summary14Job.addArguments("-in_assemb=075.assembly.coverage")
summary14Job.addArguments("-output=700.annotation.function.summary")
summary14Job.addArguments("-nr_ver=%s" % self.ach_annotation_ver)
summary14Job.addArguments("-type=function")
summary14Job.uses("075.assembly.coverage", link=Link.INPUT)
summary14Job.uses("550.cluster.aa%s.mapping" % self.aa_pid, link=Link.INPUT)
summary14Job.uses("650.aa.expand.protein", link=Link.INPUT)
summary14Job.uses("440.cluster.rna%s.mapping" % self.rna_pid, link=Link.INPUT)
summary14Job.uses("450.rna.expand.rna", link=Link.INPUT)
summary14Job.uses("700.annotation.function.summary", link=Link.OUTPUT, transfer=True)
summary14Job.profile("globus", "maxwalltime", "30")
dax.addJob(summary14Job)
dax.depends(summary14Job, qcJob)
dax.depends(summary14Job, cluster1Job)
dax.depends(summary14Job, cluster2Job)
dax.depends(summary14Job, annotatesims1Job)
dax.depends(summary14Job, annotatesims2Job)
# Annotate Summary Job (15)
summary15Job = Job("wrapper-summary", node_label="wrapper-summary")
summary15Job.addArguments("-job=1")
summary15Job.addArguments("-in_expand=650.aa.expand.protein")
summary15Job.addArguments("-in_expand=450.rna.expand.rna")
summary15Job.addArguments("-in_maps=550.cluster.aa%s.mapping" % self.aa_pid)
summary15Job.addArguments("-in_maps=440.cluster.rna%s.mapping" % self.rna_pid)
summary15Job.addArguments("-in_assemb=075.assembly.coverage")
summary15Job.addArguments("-output=700.annotation.organism.summary")
summary15Job.addArguments("-nr_ver=%s" % self.ach_annotation_ver)
summary15Job.addArguments("-type=organism")
summary15Job.uses("075.assembly.coverage", link=Link.INPUT)
summary15Job.uses("550.cluster.aa%s.mapping" % self.aa_pid, link=Link.INPUT)
summary15Job.uses("650.aa.expand.protein", link=Link.INPUT)
summary15Job.uses("440.cluster.rna%s.mapping" % self.rna_pid, link=Link.INPUT)
summary15Job.uses("450.rna.expand.rna", link=Link.INPUT)
summary15Job.uses("700.annotation.organism.summary", link=Link.OUTPUT, transfer=True)
summary15Job.profile("globus", "maxwalltime", "30")
dax.addJob(summary15Job)
dax.depends(summary15Job, qcJob)
dax.depends(summary15Job, cluster1Job)
dax.depends(summary15Job, cluster2Job)
dax.depends(summary15Job, annotatesims1Job)
dax.depends(summary15Job, annotatesims2Job)
# Annotate Summary Job (16)
summary16Job = Job("wrapper-summary", node_label="wrapper-summary")
summary16Job.addArguments("-job=1")
summary16Job.addArguments("-in_expand=650.aa.expand.lca")
summary16Job.addArguments("-in_expand=450.rna.expand.lca")
summary16Job.addArguments("-in_maps=550.cluster.aa%s.mapping" % self.aa_pid)
summary16Job.addArguments("-in_maps=440.cluster.rna%s.mapping" % self.rna_pid)
summary16Job.addArguments("-in_assemb=075.assembly.coverage")
summary16Job.addArguments("-output=700.annotation.lca.summary")
summary16Job.addArguments("-nr_ver=%s" % self.ach_annotation_ver)
summary16Job.addArguments("-type=lca")
summary16Job.uses("075.assembly.coverage", link=Link.INPUT)
summary16Job.uses("550.cluster.aa%s.mapping" % self.aa_pid, link=Link.INPUT)
summary16Job.uses("650.aa.expand.lca", link=Link.INPUT)
summary16Job.uses("440.cluster.rna%s.mapping" % self.rna_pid, link=Link.INPUT)
summary16Job.uses("450.rna.expand.lca", link=Link.INPUT)
summary16Job.uses("700.annotation.lca.summary", link=Link.OUTPUT, transfer=True)
summary16Job.profile("globus", "maxwalltime", "30")
dax.addJob(summary16Job)
dax.depends(summary16Job, qcJob)
dax.depends(summary16Job, cluster1Job)
dax.depends(summary16Job, cluster2Job)
dax.depends(summary16Job, annotatesims1Job)
dax.depends(summary16Job, annotatesims2Job)
# Annotate Summary Job (17)
summary17Job = Job("wrapper-summary", node_label="wrapper-summary")
summary17Job.addArguments("-job=1")
summary17Job.addArguments("-in_expand=650.aa.expand.ontology")
summary17Job.addArguments("-in_maps=550.cluster.aa%s.mapping" % self.aa_pid)
summary17Job.addArguments("-in_assemb=075.assembly.coverage")
summary17Job.addArguments("-output=700.annotation.ontology.summary")
summary17Job.addArguments("-nr_ver=%s" % self.ach_annotation_ver)
summary17Job.addArguments("-type=ontology")
summary17Job.uses("075.assembly.coverage", link=Link.INPUT)
summary17Job.uses("550.cluster.aa%s.mapping" % self.aa_pid, link=Link.INPUT)
summary17Job.uses("650.aa.expand.ontology", link=Link.INPUT)
summary17Job.uses("700.annotation.ontology.summary", link=Link.OUTPUT, transfer=True)
summary17Job.profile("globus", "maxwalltime", "30")
dax.addJob(summary17Job)
dax.depends(summary17Job, qcJob)
dax.depends(summary17Job, cluster1Job)
dax.depends(summary17Job, annotatesims1Job)
# Annotate Summary Job (18)
summary18Job = Job("wrapper-summary", node_label="wrapper-summary")
summary18Job.addArguments("-job=1")
summary18Job.addArguments("-in_expand=650.aa.expand.protein")
summary18Job.addArguments("-in_expand=450.rna.expand.rna")
summary18Job.addArguments("-in_maps=550.cluster.aa%s.mapping" % self.aa_pid)
summary18Job.addArguments("-in_maps=440.cluster.rna%s.mapping" % self.rna_pid)
summary18Job.addArguments("-in_assemb=075.assembly.coverage")
summary18Job.addArguments("-output=700.annotation.source.stats")
summary18Job.addArguments("-nr_ver=%s" % self.ach_annotation_ver)
summary18Job.addArguments("-type=source")
summary18Job.uses("075.assembly.coverage", link=Link.INPUT)
summary18Job.uses("550.cluster.aa%s.mapping" % self.aa_pid, link=Link.INPUT)
summary18Job.uses("650.aa.expand.protein", link=Link.INPUT)
summary18Job.uses("440.cluster.rna%s.mapping" % self.rna_pid, link=Link.INPUT)
summary18Job.uses("450.rna.expand.rna", link=Link.INPUT)
summary18Job.uses("700.annotation.source.stats", link=Link.OUTPUT, transfer=True)
summary18Job.profile("globus", "maxwalltime", "30")
dax.addJob(summary18Job)
dax.depends(summary18Job, qcJob)
dax.depends(summary18Job, cluster1Job)
dax.depends(summary18Job, cluster2Job)
dax.depends(summary18Job, annotatesims1Job)
dax.depends(summary18Job, annotatesims2Job)
# Write the DAX file
dax.writeXMLFile(self.daxfile)
# Generate the replica catalog
self.generate_replica_catalog()
def main():
if len(sys.argv) < 4:
raise Exception("Usage: %s CONFIGFILE OUTDIR METAGENOMEFILE" % sys.argv[0])
configfile = sys.argv[1]
outdir = sys.argv[2]
mgfile = sys.argv[3]
if not os.path.isfile(configfile):
raise Exception("No such file: %s" % configfile)
if os.path.isdir(outdir):
raise Exception("Directory exists: %s" % outdir)
if not os.path.isfile(mgfile):
raise Exception("No such file: %s" % mgfile)
# Create the output directory
outdir = os.path.abspath(outdir)
os.makedirs(outdir)
# Read the config file
config = ConfigParser()
config.read(configfile)
# Generate the workflow in outdir based on the config file
workflow = MGRASTWorkflow(outdir, config, mgfile)
workflow.generate_workflow()
if __name__ == '__main__':
main()