def build_report():
'''build report from scratch.
Any existing report will be overwritten.
'''
E.info("starting report build process from scratch")
P.run_report(clean=True)
def build_report():
'''build report from scratch.
Any existing report will be overwritten.
'''
E.info("starting report build process from scratch")
P.run_report(clean=True)
def build_report():
'''build report from scratch.
Any existing report will be overwritten.
Currently report function is not active for this pipeline
'''
E.info("starting report build process from scratch")
P.run_report(clean=True)
def update_report():
'''update report.'''
E.info("Updating Mapping Reported")
statement = '''cd mapping.dir;
python %(pipelinedir)s/pipeline_mapping.py
-v5 -p1 make update_report '''
E.info("updating report")
P.run_report(clean=False)
def build_report():
'''build report from scratch.
Any existing report will be overwritten.
Currently report function is not active for this pipeline
'''
E.info("starting report build process from scratch")
P.run_report(clean=True)
def update_report():
'''update report.
This will update a report with any changes inside the report
document or code. Note that updates to the data will not cause
relevant sections to be updated. Use the cgatreport-clean utility
first.
'''
E.info("updating report")
P.run_report(clean=False)
def update_report():
'''update report.
This will update a report with any changes inside the report
document or code. Note that updates to the data will not cause
relevant sections to be updated. Use the cgatreport-clean utility
first.
'''
E.info("updating report")
P.run_report(clean=False)
def build_report():
'''build report from scratch.'''
try:
os.symlink(os.path.abspath("conf.py"),
os.path.join(os.path.abspath("mapping.dir"), "conf.py"))
except OSError as e:
E.warning(str(e))
E.info("Running mapping report build from scratch")
# statement = '''cd mapping.dir;
# python %(scripts_dir)s/CGATPipelines/pipeline_mapping.py
# -v5 -p1 make build_report '''
# P.run()
E.info("starting report build process from scratch")
P.run_report(clean=True)
def build_report():
'''build report from scratch.'''
try:
os.symlink(os.path.abspath("conf.py"),
os.path.join(
os.path.abspath("mapping.dir"), "conf.py"))
except OSError as e:
E.warning(str(e))
E.info("Running mapping report build from scratch")
# statement = '''cd mapping.dir;
# python %(scripts_dir)s/CGATPipelines/pipeline_mapping.py
# -v5 -p1 make build_report '''
# P.run()
E.info("starting report build process from scratch")
P.run_report(clean = True)
def update_report():
"""update report."""
E.info("updating documentation")
P.run_report(clean=False)
def update_report():
"""update report."""
E.info("updating report")
P.run_report(clean=False)
def update_report():
'''update report.'''
E.info("updating documentation")
P.run_report(clean=False)
def update_report():
'''update report.'''
E.info("updating report")
P.run_report(clean=False)
def build_report():
'''build report from scratch.'''
E.info("starting report build process from scratch")
P.run_report(clean=True)
def build_report():
'''build report from scratch.'''
E.info("starting report build process from scratch")
P.run_report(clean=True)
def build_report():
"""build report from scratch."""
E.info("starting documentation build process from scratch")
P.run_report(clean=True)
# Generic pipeline tasks
@follows(xxx)
def full():
pass
##################################################################
# ---------------------------------------------------
# Generic pipeline tasks for CGATReport:
@follows(mkdir("report"))
def build_report():
'''build report from scratch. Any existing report will be overwritten.'''
E.info("starting report build process from scratch")
P.run_report(clean=True)
@follows(mkdir("report"))
def update_report():
'''update report.
This will update a report with any changes inside the report
document or code. Note that updates to the data will not cause
relevant sections to be updated. Use the cgatreport-clean utility
first.
'''
E.info("updating report")
P.run_report(clean=False)
@follows(update_report)
def update_report():
'''update report.'''
E.info("updating report")
P.run_report(clean=False)
def update_report():
'''update report.'''
E.info("updating documentation")
P.run_report(clean=False)
