diff --git a/README.Rmd b/README.Rmd index 5de7a98..37b09a2 100644 --- a/README.Rmd +++ b/README.Rmd @@ -30,10 +30,20 @@ github_pages_url <- description$GITHUB_PAGES **General Disclaimer**: This repository was created for use by CDC programs to collaborate on public health related projects in support of the [CDC mission](https://www.cdc.gov/about/organization/mission.htm). GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise. +# [Documentation](`r github_pages_url`/index.html) + ## Overview ``r program`` 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. +## Contacts + +| Role | Contact | +| ---------- | ------- | +| Creator | [Dakota Howard](https://github.com/dthoward96), [Reina Chau](https://github.com/rchau88) | +| Maintainer | [Dakota Howard](https://github.com/dthoward96) | +| Back-Up | [Reina Chau](https://github.com/rchau88), [Brian Lee](https://github.com/leebrian) | + ## Prerequisites - **NCBI Submissions** @@ -93,6 +103,10 @@ Before submitters can perform a batch submission using ``r program``, they must - [How to run seqsender with Compose](`r github_pages_url`/articles/compose_installation.html) - [How to run seqsender with Singularity](`r github_pages_url`/articles/singularity_installation.html) +## Code Attributions + +Dakota Howard and Reina Chau for majority of the code base with input and testing from [colleagues](`r github_pages_url`/authors.html). + ## Public Domain Standard Notice 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 [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/). 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. diff --git a/README.md b/README.md index b02dd5c..355b377 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,19 @@ + + +

+ Public Database Submission Pipeline +

**Beta Version**: 1.1.0. 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! +Feedback and suggestions are welcome\! **General Disclaimer**: This repository was created for use by CDC programs to collaborate on public health related projects in support of @@ -18,6 +23,8 @@ CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise. +# [Documentation](https://cdcgov.github.io/seqsender/index.html) + ## Overview `seqsender` is a Python program that is developed to automate the @@ -29,9 +36,17 @@ 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. +## Contacts + +| Role | Contact | +| ---------- | ---------------------------------------------------------------------------------------- | +| Creator | [Dakota Howard](https://github.com/dthoward96), [Reina Chau](https://github.com/rchau88) | +| Maintainer | [Dakota Howard](https://github.com/dthoward96) | +| Back-Up | [Reina Chau](https://github.com/rchau88), [Brian Lee](https://github.com/leebrian) | + ## Prerequisites -- **NCBI Submissions** + - **NCBI Submissions** `seqsender` utilizes an UI-Less Data Submission Protocol to bulk upload submission files (e.g., *submission.xml*, *submission.zip*, etc.) to @@ -63,11 +78,11 @@ FTP on the command line. Before attempting to submit a submission using gb-admin@ncbi.nlm.nih.gov to discuss requirements for submissions. -5. Coordinate a NCBI namespace name (**spuid_namespace**) that will be +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 + 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. For more information about these two fields, see @@ -78,7 +93,9 @@ FTP on the command line. Before attempting to submit a submission using [GENBANK](https://cdcgov.github.io/seqsender/articles/genbank_submission.html#metadata) metadata requirements. -- **GISAID Submissions** + + + - **GISAID Submissions** `seqsender` makes use of GISAID’s Command Line Interface tools to bulk uploading meta- and sequence-data to GISAID databases. Presently, the @@ -145,14 +162,20 @@ prepared and stored in a submission directory of choice. ## Quick Start -- [How to run seqsender - locally](https://cdcgov.github.io/seqsender/articles/local_installation.html) -- [How to run seqsender with - Docker](https://cdcgov.github.io/seqsender/articles/docker_installation.html) -- [How to run seqsender with - Compose](https://cdcgov.github.io/seqsender/articles/compose_installation.html) -- [How to run seqsender with - Singularity](https://cdcgov.github.io/seqsender/articles/singularity_installation.html) + - [How to run seqsender + locally](https://cdcgov.github.io/seqsender/articles/local_installation.html) + - [How to run seqsender with + Docker](https://cdcgov.github.io/seqsender/articles/docker_installation.html) + - [How to run seqsender with + Compose](https://cdcgov.github.io/seqsender/articles/compose_installation.html) + - [How to run seqsender with + Singularity](https://cdcgov.github.io/seqsender/articles/singularity_installation.html) + +## Code Attributions + +Dakota Howard and Reina Chau for majority of the code base with input +and testing from +[colleagues](https://cdcgov.github.io/seqsender/authors.html). ## Public Domain Standard Notice