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/shiny/* | ||
/vignettes/* | ||
/docs/* |
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--- | ||
name: Bug report | ||
about: Create a report to help us improve | ||
title: '' | ||
labels: '' | ||
assignees: '' | ||
about: Create a report to help us improve SeqSender | ||
title: "[BUG]" | ||
labels: bug | ||
assignees: dthoward96 | ||
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--- | ||
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**Describe the bug** | ||
A clear and concise description of what feature is not working. | ||
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**Impact** | ||
Please describe the impact this bug is causing to your program or organization. | ||
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**To Reproduce** | ||
Steps to reproduce the behavior: | ||
1. Go to '...' | ||
2. Click on '....' | ||
3. Scroll down to '....' | ||
4. See error | ||
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**Expected behavior** | ||
A clear and concise description of what you expected to happen. | ||
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**Screenshots** | ||
If applicable, add screenshots to help explain your problem. | ||
- Which databases are you attempting submission to? | ||
- Is the error related to a specific database/metadata field? If so, which? | ||
- Steps to reproduce the behavior: | ||
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**Logs** | ||
If applicable, please attach logs to help describe your problem. | ||
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**Desktop (please complete the following information):** | ||
- OS: [e.g. iOS] | ||
- Browser [e.g. chrome, safari] | ||
- Version [e.g. 22] | ||
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**Smartphone (please complete the following information):** | ||
- Device: [e.g. iPhone6] | ||
- OS: [e.g. iOS8.1] | ||
- Browser [e.g. stock browser, safari] | ||
- Version [e.g. 22] | ||
**Version** | ||
- Version Number: [e.g. v1.2.0.] | ||
- SeqSender Version: [e.g. Singularity, Docker, Script] | ||
- OS [e.g. Linux, Mac] | ||
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**Additional context** | ||
Add any other context about the problem here. |
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--- | ||
name: Feature request | ||
about: Suggest an idea for this project | ||
title: '' | ||
labels: '' | ||
about: Suggest a new feature for SeqSender | ||
title: "[FEATURE REQUEST]" | ||
labels: enhancement | ||
assignees: '' | ||
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--- | ||
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**Is your feature request related to a problem? Please describe.** | ||
**Is this feature for general SeqSender usage or for submitting to a specific database, if so what database?** | ||
SeqSender or a specified database name. | ||
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**Is your feature request related to a problem? If so please describe.** | ||
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] | ||
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**Describe the solution you'd like** | ||
A clear and concise description of what you want to happen. | ||
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**Describe alternatives you've considered** | ||
A clear and concise description of any alternative solutions or features you've considered. | ||
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**Additional context** | ||
Add any other context or screenshots about the feature request here. |
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--- | ||
name: General | ||
about: SeqSender Issue | ||
title: '' | ||
labels: '' | ||
assignees: '' | ||
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--- | ||
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**Is this related to a specific database? If so, which database?** | ||
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**Describe your issue below:** |
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</p> | ||
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**Beta Version**: 1.2.0. This pipeline is currently in Beta testing, and | ||
**Beta Version**: 1.2.1. This pipeline is currently in Beta testing, and | ||
issues could appear during submission. Please use it at your own risk. | ||
Feedback and suggestions are welcome\! | ||
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CDC use of GitHub does not imply an endorsement of any one particular | ||
service, product, or enterprise. | ||
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# [Documentation](https://dthoward96.github.io/seqsender_test_website/) | ||
# [Documentation](https://cdcgov.github.io/seqsender/) | ||
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## Overview | ||
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| Maintainer | [Dakota Howard](https://github.com/dthoward96) | | ||
| Back-Up | [Reina Chau](https://github.com/rchau88), [Brian Lee](https://github.com/leebrian) | | ||
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## Prerequisites | ||
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- **NCBI Submissions** | ||
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`seqsender` utilizes an UI-Less Data Submission Protocol to bulk upload | ||
submission files (e.g., *submission.xml*, *submission.zip*, etc.) to | ||
NCBI archives. The submission files are uploaded to the NCBI server via | ||
FTP on the command line. Before attempting to submit a submission using | ||
`seqsender`, submitter will need to | ||
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1. Have a NCBI account. To sign up, visit [NCBI | ||
website](https://account.ncbi.nlm.nih.gov/). | ||
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2. Required for CDC users and highly recommended for others is creating | ||
a center account for your institution/lab [NCBI Center Account | ||
Instructions](https://submit.ncbi.nlm.nih.gov/sarscov2/sra/#step6). | ||
Center accounts allow you to perform submissions UI-less submissions | ||
as your institution/lab. | ||
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3. Required for CDC users and also recommended is creating a submission | ||
group in [NCBI Submission Portal](https://submit.ncbi.nlm.nih.gov). | ||
A group should include all individuals who need access to UI-less | ||
submissions through the web interface with your center account. Each | ||
member of the group must also have an individual NCBI account. [NCBI | ||
website](https://account.ncbi.nlm.nih.gov/). | ||
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4. Refer to this page for information regarding requirements for | ||
GenBank submissions via FTP only. This page applies only for COVID | ||
and Influenza [NCBI GenBank FTP | ||
Submissions](https://submit.ncbi.nlm.nih.gov/sarscov2/genbank/#step5) | ||
For further questions contact | ||
<a href="mailto:[email protected]">[email protected]</a> | ||
to discuss requirements for submissions. | ||
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5. Coordinate a NCBI namespace name (**spuid\_namespace**) that will be | ||
used with Submitter Provided Unique Identifiers (**spuid**) in the | ||
submission. The liaison of **spuid\_namespace** and **spuid** is | ||
used to report back assigned accessions as well as for cross-linking | ||
objects within submission. The values of **spuid\_namespace** are up | ||
to the submitter to decide but they must be unique and | ||
well-coordinated prior to make a submission. | ||
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<!-- end list --> | ||
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- **GISAID Submissions** | ||
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`seqsender` makes use of GISAID’s Command Line Interface tools to bulk | ||
uploading meta- and sequence-data to GISAID databases. Presently, the | ||
pipeline supports upload to EpiFlu (**Influenza A Virus**), EpiCoV | ||
(**SARS-COV-2**), EpiPox (**Monkeypox**), and EpiArbo (**Arbovirus**). | ||
Before uploading, submitter needs to | ||
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1. Have a GISAID account. To sign up, visit [GISAID | ||
Platform](https://gisaid.org/). | ||
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2. Request a client-ID for your specified Epi(Flu/CoV/Pox/Arbo) | ||
database in order to use its CLI tool. The CLI utilizes the | ||
client-ID along with the username and password to authenticate the | ||
database prior to make a submission. To obtain a client-ID, please | ||
<a href="mailto:[email protected]" >[email protected]</a> to | ||
request. ***Important note**: If submitter would like to upload a | ||
“test” submission first to familiarize themselves with the | ||
submission process prior to make a real submission, one should | ||
additionally request a test client-id to perform such submissions.* | ||
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3. Download the | ||
<a href="https://cdcgov.github.io/seqsender/articles/images/fluCLI_download.png" target="_blank">EpiFlu</a> | ||
or | ||
<a href="https://cdcgov.github.io/seqsender/articles/images/covCLI_download.png" target="_blank">EpiCoV</a> | ||
CLI from the **GISAID platform** and stored them in the destination | ||
of choice prior to perform a batch upload. | ||
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Here is a quick look of where to store the downloaded **GISAID CLI** | ||
package. | ||
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![](man/figures/gisaid_cli_dir.png) | ||
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## Code Attributions | ||
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Dakota Howard and Reina Chau for majority of the code base with input | ||
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