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V1.2.0 Prod Update #60

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merged 3 commits into from
Aug 6, 2024
Merged

V1.2.0 Prod Update #60

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2d57f7f
Update Dev to v1.2.0 (#59)
dthoward96 Aug 6, 2024
b8b22c4
V1.2.0 Prod Update
dthoward96 Aug 6, 2024
8382298
Merge branch 'master' into dev
dthoward96 Aug 6, 2024
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1 change: 0 additions & 1 deletion gisaid_handler.py
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion shiny/index.py
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Expand Up @@ -6,7 +6,7 @@
ui.HTML(
"""
<h2>Overview</h2>
<p><code>seqsender</code> is a Python program that is developed to automate the process of generating necessary submission files and batch uploading them to <ins>NCBI archives</ins> (such as <strong>BioSample</strong>, <strong>SRA</strong>, and <strong>Genbank</strong>) and <ins>GISAID databases</ins> (e.g. <strong>EpiFlu</strong> and <strong>EpiCoV</strong>). Presently, the pipeline is capable of uploading <strong>Influenza A Virus</strong> (FLU) and <strong>SARS-COV-2</strong> (COV) data. However, the dynamic nature of this pipeline can allow for additional uploads of other organisms in future updates or requests.</p>
<p><code>seqsender</code> is a Python program that is developed to automate the process of generating necessary submission files and batch uploading them to <ins>NCBI archives</ins> (such as <strong>BioSample</strong>, <strong>SRA</strong>, and <strong>Genbank</strong>) and <ins>GISAID databases</ins> (e.g. <strong>EpiFlu</strong>, <strong>EpiPox</strong>, and <strong>EpiCoV</strong>).</p>
<h2>Public Domain Standard Notice</h2>
<p>This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the <a href="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 Universal public domain dedication</a>. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.</p>
<h2>License Standard Notice</h2>
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