def upload_tenx(sampleid, before, finished): print("Calling upload.") tenx = TenxAnalysis("./{}/outs/".format(sampleid)) tenx.finalize() tenxds = TenxDataStorage(sampleid) tenxds.upload_cellranger(tenx) open(finished, "w").write("Completed")
def Run(sampleid, finished): if not os.path.exists("cellranger.complete"): CellRanger.count([sampleid]) tenx = TenxAnalysis("./{}/outs/".format(sampleid)) tenx.finalize() tenxds = TenxDataStorage(sampleid) tenxds.upload_cellranger(tenx) open(finished,"w").write("Completed")
def RunUpload(sampleid, finished, species): print("Uploading ",species, sampleid) tenx_output = os.path.join(config.jobpath,"{}/outs/".format(sampleid)) tenx = TenxAnalysis(tenx_output) tenx.finalize() tenxds = TenxDataStorage(sampleid, species=species) print("Running upload") tenxds.upload_cellranger(tenx) open(finished,"w").write("Completed")
def upload(self, tenx): outs = self.get_output() tenx = TenxAnalysis(outs) tenx.finalize() storage = DataStorage(self.prefix) storage.upload_results(tenx)