def publish():
'''publish files.'''
# publish web pages
P.publish_report()
# publish additional data
web_dir = PARAMS["web_dir"]
project_id = P.getProjectId()
# directory, files
exportfiles = {
"intervals": glob.glob(os.path.join(
PARAMS["exportdir"], "bed", "*.bed.gz")) +
glob.glob(os.path.join(PARAMS["exportdir"], "bed", "*.bed.gz.tbi")),
}
bams = []
for targetdir, filenames in exportfiles.iteritems():
if len(filenames) == 0:
E.warn("no files for target '%s'" % targetdir)
for src in filenames:
dest = "%s/%s/%s" % (web_dir, targetdir, os.path.basename(src))
if dest.endswith(".bam"):
bams.append(dest)
dest = os.path.abspath(dest)
destdir = os.path.dirname(dest)
if not os.path.exists(destdir):
os.makedirs(destdir)
if not os.path.exists(dest):
E.debug("creating symlink from %s to %s" % (src, dest))
os.symlink(os.path.abspath(src), dest)
def publish():
'''publish files.'''
# publish web pages
P.publish_report()
# publish additional data
web_dir = PARAMS["web_dir"]
project_id = P.getProjectId()
# directory, files
exportfiles = {
"intervals":
glob.glob(os.path.join(PARAMS["exportdir"], "bed", "*.bed.gz")) +
glob.glob(os.path.join(PARAMS["exportdir"], "bed", "*.bed.gz.tbi")),
}
bams = []
for targetdir, filenames in exportfiles.items():
if len(filenames) == 0:
E.warn("no files for target '%s'" % targetdir)
for src in filenames:
dest = "%s/%s/%s" % (web_dir, targetdir, os.path.basename(src))
if dest.endswith(".bam"):
bams.append(dest)
dest = os.path.abspath(dest)
destdir = os.path.dirname(dest)
if not os.path.exists(destdir):
os.makedirs(destdir)
if not os.path.exists(dest):
E.debug("creating symlink from %s to %s" % (src, dest))
os.symlink(os.path.abspath(src), dest)
def publish():
'''publish files.'''
# publish web pages
patterns = [(re.compile("/ifs/projects/proj012/report/html"),
"http://www.cgat.org/downloads/KW0ok5WWly/report"),
]
P.publish_report(patterns=patterns)
def publish():
'''publish files.'''
# publish web pages
patterns = [
(re.compile("/ifs/projects/proj012/report/html"),
"http://www.cgat.org/downloads/KW0ok5WWly/report"),
]
P.publish_report(patterns=patterns)
def publish():
'''publish files.'''
# publish web pages
P.publish_report()
# publish additional data - i.e. the final lncRNA gtf file
web_dir = PARAMS["web_dir"]
if not os.path.exists(os.path.join(web_dir), "lncrna_final.class.gtf.gz"):
os.symlink("lncrna_final.class.gtf.gz", os.path.abspath(
os.path.join(os.path.join(web_dir), "lncrna_final.class.gtf.gz")))
def publish():
'''publish files.'''
# publish web pages
P.publish_report()
# publish additional data - i.e. the final lncRNA gtf file
web_dir = PARAMS["web_dir"]
if not os.path.exists(os.path.join(web_dir), "lncrna_final.class.gtf.gz"):
os.symlink("lncrna_final.class.gtf.gz", os.path.abspath(
os.path.join(os.path.join(web_dir), "lncrna_final.class.gtf.gz")))
def publish():
'''publish files.'''
# publish web pages
P.publish_report()
# publish additional data
web_dir = PARAMS["web_dir"]
project_id = P.getProjectId()
ucsc_urls = {
"bam":
"""track type=bam name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/%(dirname)s/%(filename)s""",
"bigwig":
"""track type=bigWig name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/%(dirname)s/%(filename)s""",
}
# directory, files
exportfiles = (
("bamfiles", glob.glob("*/*.genome.bam") +
glob.glob("*/*.genome.bam.bai"), "bam"),
("bamfiles", glob.glob("*/*.prep.bam") +
glob.glob("*/*.prep.bam.bai"), "bam"),
("medips", glob.glob("*/*.bigwig"), "bigwig"),
)
ucsc_files = []
for targetdir, filenames, datatype in exportfiles:
for src in filenames:
filename = os.path.basename(src)
dest = "%s/%s/%s" % (web_dir, targetdir, filename)
suffix = os.path.splitext(src)
if suffix in ucsc_urls:
ucsc_files.append((datatype, targetdir, filename))
dest = os.path.abspath(dest)
if not os.path.exists(dest):
os.symlink(os.path.abspath(src), dest)
# output ucsc links
for ucsctype, dirname, filename in ucsc_files:
filename = os.path.basename(filename)
track = P.snip(filename, ucsctype)
print(ucsc_urls[ucsctype] % locals())
def publish():
'''publish files.'''
# publish web pages
P.publish_report()
# publish additional data
web_dir = PARAMS["web_dir"]
project_id = P.getProjectId()
ucsc_urls = {
"bam":
"""track type=bam name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/%(dirname)s/%(filename)s""",
"bigwig":
"""track type=bigWig name="%(track)s" bigDataUrl=http://www.cgat.org/downloads/%(project_id)s/%(dirname)s/%(filename)s""",
}
# directory, files
exportfiles = (
("bamfiles",
glob.glob("*/*.genome.bam") + glob.glob("*/*.genome.bam.bai"), "bam"),
("bamfiles", glob.glob("*/*.prep.bam") + glob.glob("*/*.prep.bam.bai"),
"bam"),
("medips", glob.glob("*/*.bigwig"), "bigwig"),
)
ucsc_files = []
for targetdir, filenames, datatype in exportfiles:
for src in filenames:
filename = os.path.basename(src)
dest = "%s/%s/%s" % (web_dir, targetdir, filename)
suffix = os.path.splitext(src)
if suffix in ucsc_urls:
ucsc_files.append((datatype, targetdir, filename))
dest = os.path.abspath(dest)
if not os.path.exists(dest):
os.symlink(os.path.abspath(src), dest)
# output ucsc links
for ucsctype, dirname, filename in ucsc_files:
filename = os.path.basename(filename)
track = P.snip(filename, ucsctype)
print(ucsc_urls[ucsctype] % locals())
def publish():
'''publish files.'''
# directory, files
export_files = {"bigwigfiles": glob.glob("*/*.bigwig")}
if PARAMS['ucsc_exclude']:
for filetype, files in export_files.items():
new_files = set(files)
for f in files:
for regex in P.asList(PARAMS['ucsc_exclude']):
if re.match(regex, f):
new_files.remove(f)
break
export_files[filetype] = list(new_files)
# publish web pages
E.info("publishing report")
P.publish_report(export_files=export_files)
E.info("publishing UCSC data hub")
P.publish_tracks(export_files)
def publish():
'''publish files.'''
P.publish_report()
def publish():
'''publish report and data.'''
E.info("publishing report")
P.publish_report()
def publish():
'''publish files.'''
# publish web pages
P.publish_report()
def publish():
"""publish files."""
P.publish_report()
def publish_report():
"""publish report."""
E.info("publishing report")
P.publish_report()
def publish_report():
"""publish report in the CGAT downloads directory."""
E.info("publishing report")
P.publish_report()
def publish():
'''publish report and data.'''
E.info( "publishing report" )
P.publish_report()
def publish_report():
'''publish report in the CGAT downloads directory.'''
E.info("publishing report")
P.publish_report()
def publish_report():
'''publish report.'''
E.info("publishing report")
P.publish_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 publish_report():
'''publish report in the CGAT downloads directory.'''
E.info("publishing report")
P.publish_report()
##################################################################
# ---------------------------------------------------
# See Steve's way of reporting:
# https://github.com/snsansom/scseq/blob/master/pipelines/pipeline_scrnaseq.py
# --------------------- < generic pipeline tasks > -------------------------- #
'''
@follows(mkdir("notebook.dir"))
@transform(glob.glob(os.path.join(os.path.dirname(__file__),
"pipeline_notebooks",
os.path.basename(__file__)[:-len(".py")],
"*")),
regex(r".*/(.*)"),
def publish_report():
'''publish report in the CGAT downloads directory.'''
E.info("publishing report")
P.publish_report()
def publish():
'''publish files.'''
P.publish_report()
def publish_report():
'''publish report.'''
E.info("publishing report")
P.publish_report()
def publish():
'''publish files.'''
# publish web pages
P.publish_report()
