diff --git a/gisaid_handler.py b/gisaid_handler.py index 2fa3c64..06e65fc 100755 --- a/gisaid_handler.py +++ b/gisaid_handler.py @@ -97,7 +97,6 @@ def submit_gisaid(organism: str, submission_dir: str, submission_name: str, conf gisaid_cli = file_handler.validate_gisaid_installer(submission_dir=submission_dir, organism=organism) print(f"Uploading sample files to GISAID-{organism}, as a '{submission_type}' submission. If this is not intended, interrupt immediately.", file=sys.stdout) time.sleep(5) - sub = process_gisaid_log(log_file=os.path.join(submission_dir, "gisaid_upload_log_" + str(1) + ".txt"), submission_dir=submission_dir) # Set number of attempt to 3 if erroring out occurs attempts = 1 # Submit to GISAID diff --git a/shiny/index.py b/shiny/index.py index 68a5e90..fbe0ea8 100755 --- a/shiny/index.py +++ b/shiny/index.py @@ -6,7 +6,7 @@ ui.HTML( """
seqsender
is a Python program that is developed to automate the process of generating necessary submission files and batch uploading them to NCBI archives (such as BioSample, SRA, and Genbank) and GISAID databases (e.g. EpiFlu and EpiCoV). Presently, the pipeline is capable of uploading Influenza A Virus (FLU) and SARS-COV-2 (COV) data. However, the dynamic nature of this pipeline can allow for additional uploads of other organisms in future updates or requests.
seqsender
is a Python program that is developed to automate the process of generating necessary submission files and batch uploading them to NCBI archives (such as BioSample, SRA, and Genbank) and GISAID databases (e.g. EpiFlu, EpiPox, and EpiCoV).
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