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Add how to report bugs section #8

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Add how to report bugs section
christiam Jul 6, 2020
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Fix TOC, refine instructions for bug reporting
christiam Jul 7, 2020
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Merge branch 'master' into how-to-report-bugs
christiam Jul 7, 2020
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Simplify TOC
christiam Jul 7, 2020
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Simplify TOC
christiam Jul 7, 2020
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41 changes: 17 additions & 24 deletions README.md
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Expand Up @@ -8,40 +8,28 @@ This repository contains documentation for the [NCBI BLAST+](https://www.ncbi.nl
* [What Is Cloud Computing?](#what-is-cloud-computing)
* [What Is Docker?](#what-is-docker)
* [Google Cloud Platform Setup](#google-cloud-platform-setup)
* [Section 1 - Getting Started Using the BLAST+ Docker Image with A Small Example](#section-1---getting-started-using-the-blast-docker-image-with-a-small-example)
* [Section 2 - A Step-by-Step Guide Using the BLAST+ Docker Image](#section-2---a-step-by-step-guide-using-the-blast-docker-image)
* [Step 1. Install Docker](#step-1-install-docker)
* [Docker `run` command options](#docker-run-command-options)
* [Docker `run` command structure](#docker-run-command-structure)
* [Useful Docker commands](#useful-docker-commands)
* [Using BLAST+ with Docker](#using-blast-with-docker)
* [Versions of BLAST+ Docker image](#versions-of-blast-docker-image)
* [Supported tags](#supported-tags)
* [Step 2. Import sequences and create a BLAST database](#step-2---import-sequences-and-create-a-blast-database)
* [Show BLAST databases available for download from the Google Cloud bucket](#show-blast-databases-available-for-download-from-the-google-cloud-bucket)
* [Show BLAST databases available for download from NCBI](#show-blast-databases-available-for-download-from-ncbi)
* [Show available BLAST databases on local host](#show-available-blast-databases-on-local-host)
* [Step 3. Run BLAST](#step-3-run-blast)
* [Stop the GCP instance](#stop-the-gcp-instance)
* [Section 3 - Using the BLAST+ Docker Image at Production Scale](#section-3---using-the-blast-docker-image-at-production-scale)
* [Background](#background)
* [BLAST+ Docker image benchmarks](#blast-docker-image-benchmarks)
* [Commands to run](#commands-to-run)
* [Section 1 - Getting Started Using the BLAST Docker Image with a Small Example](#section-1---getting-started-using-the-blast-docker-image-with-a-small-example)
* [Section 2 - A Step-by-Step Guide Using the BLAST Docker Image](#section-2---a-step-by-step-guide-using-the-blast-docker-image)
* [Section 3 - Using the BLAST Docker Image at Production Scale](#section-3---using-the-blast-docker-image-at-production-scale)
* [Amazon Web Services Setup](#amazon-web-services-setup)
* [Overview](#overview)
* [Requirements](#requirements-1)
* [Example 1: Run BLAST+ Docker on an Amazon EC2 Virtual Machine](#example-1-run-blast-docker-on-an-amazon-ec2-virtual-machine)
* [Example 2: Run BLAST+ Docker on an Amazon EC2 Virtual Machine - Protein Data Bank Amino Acid DB](#example-2-run-blast-docker-on-an-amazon-ec2-virtual-machine---protein-data-bank-amino-acid-db)
* [Example 3: Run BLAST+ Docker on AWS Fargate](#example-3-run-blast-docker-on-aws-fargate)
* [Example 4: Run BLAST+ Docker on AWS Fargate at Scale Using Step and Batch Functions](#example-4-run-blast-docker-on-aws-fargate-at-scale-using-step-and-batch-functions)
* [Appendix](#appendix)
* [Appendix A: Transfer Files to/from an AWS VM](#appendix-a-transfer-files-tofrom-an-aws-vm)
* [Appendix A: Transfer Files to/from an AWS VM](#appendix-a-transfer-files-tofrom-an-aws-vm)
* [Additional Resources](#additional-resources)
* [Maintainer](#maintainer)
* [How to report bugs?](#how-to-report-bugs)
* [License](#license)
* [Appendix](#appendix)
* [Appendix A. Cloud and Docker Concepts](#appendix-a-cloud-and-docker-concepts)
* [Appendix B. Alternative Ways to Run Docker](#appendix-b-alternative-ways-to-run-docker)
* [Appendix C. Transfer files to/from a GCP VM](#appendix-c-transfer-files-tofrom-a-gcp-vm)
* [Appendix](#appendix-1)
* [Appendix A. Cloud and Docker Concepts](#appendix-a-cloud-and-docker-concepts)
* [Appendix B. Alternative Ways to Run Docker](#appendix-b-alternative-ways-to-run-docker)
* [Run BLAST Docker image interactively](#run-blast-docker-image-interactively)
* [Run BLAST Docker image in detached mode](#run-blast-docker-image-in-detached-mode)
* [Appendix C. Transfer Files to/from a GCP VM](#appendix-c-transfer-files-tofrom-a-gcp-vm)

# What Is NCBI BLAST?
<img src="./images/nih_nlm_ncbi_logo.png" alt="ncbi-logo" width="25%" height="25%" />
Expand Down Expand Up @@ -815,6 +803,11 @@ or [email us.](mailto:blast-help@ncbi.nlm.nih.gov)
[National Library of Medicine (NLM)](https://www.nlm.nih.gov/)
[National Institutes of Health (NIH)](https://www.nih.gov/)

# How to report bugs?

Please provide us with the information in steps 1-4 via email(mailto:blast-help@ncbi.nlm.nih.gov) from [How do I report BLAST+
problems?](https://support.nlm.nih.gov/knowledgebase/article/KA-05184/).

# License

View refer to the [license](https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE) and [copyright](http://ncbi.github.io/blast-cloud/dev/copyright.html) information for the software contained in this image.
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