def build_report(self, params, reads_refs, alignments, alignment_set=None):
"""
Builds and uploads the HISAT2 report.
"""
report_client = KBaseReport(self.callback_url)
report_text = None
created_objects = list()
for k in alignments:
created_objects.append({
"ref":
alignments[k]["ref"],
"description":
"Reads {} aligned to Genome {}".format(k, params["genome_ref"])
})
if alignment_set is not None:
created_objects.append({
"ref": alignment_set,
"description": "Set of all new alignments"
})
report_text = "Created {} alignments from the given alignment set.".format(
len(alignments))
qm = kb_QualiMap(self.callback_url, service_ver='dev')
qc_ref = alignment_set
if qc_ref is None: # then there's only one alignment...
qc_ref = alignments[alignments.keys()[0]]["ref"]
bamqc_params = {"create_report": 0, "input_ref": qc_ref}
result = qm.run_bamqc(bamqc_params)
index_file = None
for f in os.listdir(result["qc_result_folder_path"]):
if f.endswith(".html"):
index_file = f
if index_file is None:
raise RuntimeError(
"QualiMap failed - no HTML file was found in the generated output."
)
html_zipped = package_directory(self.callback_url,
result["qc_result_folder_path"],
index_file, 'QualiMap Results')
report_params = {
"message": report_text,
"direct_html_link_index": 0,
"html_links": [html_zipped],
"report_object_name": "QualiMap-" + str(uuid.uuid4()),
"workspace_name": params["ws_name"],
"objects_created": created_objects
}
report_info = report_client.create_extended_report(report_params)
return report_info
def __init__(self, config):
self.ws_url = config["workspace-url"]
self.callback_url = config['SDK_CALLBACK_URL']
self.token = config['KB_AUTH_TOKEN']
self.shock_url = config['shock-url']
self.scratch = config['scratch']
self.srv_wiz_url = config['srv-wiz-url']
self.ws = Workspace(self.ws_url, token=self.token)
self.bt = kb_Bowtie2(self.callback_url)
self.rau = ReadsAlignmentUtils(self.callback_url)
self.qualimap = kb_QualiMap(self.callback_url)
self.ru = ReadsUtils(self.callback_url)
self.dfu = DataFileUtil(self.callback_url)
self.set_client = SetAPI(self.srv_wiz_url)
def __init__(self, scratch_dir, workspace_url, callback_url, srv_wiz_url, provenance):
self.workspace_url = workspace_url
self.callback_url = callback_url
self.srv_wiz_url = srv_wiz_url
self.au = AssemblyUtil(self.callback_url)
self.dfu = DataFileUtil(self.callback_url, service_ver='beta')
self.scratch = scratch_dir
self.working_dir = scratch_dir
self.prog_runner = Program_Runner(self.STAR_BIN, self.scratch)
self.provenance = provenance
self.ws_client = Workspace(self.workspace_url)
self.parallel_runner = KBParallel(self.callback_url)
self.qualimap = kb_QualiMap(self.callback_url, service_ver='dev')
self.set_api_client = SetAPI(self.srv_wiz_url, service_ver='dev')
self.eu = ExpressionUtils(self.callback_url, service_ver='beta')
def __init__(self, scratch_dir, workspace_url, callback_url, srv_wiz_url, provenance):
self.scratch_dir = scratch_dir
self.workspace_url = workspace_url
self.callback_url = callback_url
self.srv_wiz_url = srv_wiz_url
self.provenance = provenance
# from the provenance, extract out the version to run by exact hash if possible
self.my_version = 'release'
if len(provenance) > 0:
if 'subactions' in provenance[0]:
self.my_version = self.get_version_from_subactions('kb_Bowtie2', provenance[0]['subactions'])
print('Running kb_Bowtie2 version = ' + self.my_version)
self.ws = Workspace(self.workspace_url)
self.bowtie2 = Bowtie2Runner(self.scratch_dir)
self.parallel_runner = KBParallel(self.callback_url)
self.qualimap = kb_QualiMap(self.callback_url)
def __init__(self, config, provenance):
self.config = config
self.workspace_url = config['workspace-url']
self.callback_url = os.environ['SDK_CALLBACK_URL']
self.scratch = config['scratch']
self.srv_wiz_url = config['srv-wiz-url']
self.parallel_runner = KBParallel(self.callback_url)
self.provenance = provenance
self.star_utils = STARUtils(self.scratch, self.workspace_url,
self.callback_url, self.srv_wiz_url,
provenance)
self.set_api_client = SetAPI(self.srv_wiz_url, service_ver='dev')
self.qualimap = kb_QualiMap(self.callback_url, service_ver='dev')
self.star_idx_dir = None
self.star_out_dir = None
# from the provenance, extract out the version to run by exact hash if possible
self.my_version = 'release'
if len(provenance) > 0:
if 'subactions' in provenance[0]:
self.my_version = self.get_version_from_subactions(
'kb_STAR', provenance[0]['subactions'])
print('Running kb_STAR version = ' + self.my_version)