diff --git a/README.md b/README.md index ed0414c..72f51a4 100644 --- a/README.md +++ b/README.md @@ -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? ncbi-logo @@ -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.