From e5c269c6c206f4fc6043944060f3e72839792d21 Mon Sep 17 00:00:00 2001 From: Christiam Camacho Date: Mon, 6 Jul 2020 09:41:36 -0400 Subject: [PATCH 1/4] Add how to report bugs section --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index 303e6c7..e118555 100644 --- a/README.md +++ b/README.md @@ -38,6 +38,7 @@ This repository contains documentation for the [NCBI BLAST+](https://www.ncbi.nl * [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?](#report-to-report-bugs) * [License](#license) * [Appendix](#appendix) * [Appendix A. Cloud and Docker Concepts](#appendix-a-cloud-and-docker-concepts) @@ -818,6 +819,11 @@ 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 follow the instructions in [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. From 085c25525569b2dd6693e4c2975ecc3cf238fa1b Mon Sep 17 00:00:00 2001 From: Christiam Camacho Date: Tue, 7 Jul 2020 10:14:19 -0400 Subject: [PATCH 2/4] Fix TOC, refine instructions for bug reporting --- README.md | 85 ++++++++++++++++++++++++++++++++++--------------------- 1 file changed, 52 insertions(+), 33 deletions(-) diff --git a/README.md b/README.md index e118555..2aa2825 100644 --- a/README.md +++ b/README.md @@ -8,42 +8,61 @@ 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) + * [Requirements](#requirements) + * [Set up your GCP account and create a VM for analysis](#set-up-your-gcp-account-and-create-a-vm-for-analysis) + * [1. Creating your GCP account and registering for the free $300 credit program. (If you already have a GCP billing account, you can skip to step 2.)](#1-creating-your-gcp-account-and-registering-for-the-free-300-credit-program-if-you-already-have-a-gcp-billing-account-you-can-skip-to-step-2) + * [2. Create a Virtual Machine (VM)](#2-create-a-virtual-machine-vm) + * [3. Access a GCP VM from a local machine](#3-access-a-gcp-vm-from-a-local-machine) + * [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) * [Amazon Web Services Setup](#amazon-web-services-setup) - - * [Amazon Web Services Setup](#amazon-web-services-setup) - * [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) + * [Amazon Web Services Setup](#amazon-web-services-setup-1) + * [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) + * [Step 1: Create an EC2 Virtual Machine (VM)](#step-1-create-an-ec2-virtual-machine-vm) + * [Step 2: Establish an SSH session with the EC2 VM](#step-2-establish-an-ssh-session-with-the-ec2-vm) + * [Step 3: Import sequences and create a BLAST database](#step-3-import-sequences-and-create-a-blast-database) + * [Step 4: Run BLAST](#step-4-run-blast) + * [Step 5: Optional - Show BLAST databases available for download from the NCBI AWS bucket](#step-5-optional---show-blast-databases-available-for-download-from-the-ncbi-aws-bucket) + * [Step 6: Optional - Show BLAST databases available for download from NCBI](#step-6-optional---show-blast-databases-available-for-download-from-ncbi) + * [Step 7: Stop the EC2 VM](#step-7-stop-the-ec2-vm) + * [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) + * [Step 1: Create an EC2 Virtual Machine (VM)](#step-1-create-an-ec2-virtual-machine-vm-1) + * [Step 2: Establish an SSH session with the EC2 VM](#step-2-establish-an-ssh-session-with-the-ec2-vm-1) + * [Step 2. Retrieve sequences](#step-2-retrieve-sequences) + * [Step 3: Download Protein Data Bank Amino Acid Database (pdbaa)](#step-3-download-protein-data-bank-amino-acid-database-pdbaa) + * [Step 4: Run BLAST ](#step-4-run-blast-1) + * [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?](#report-to-report-bugs) + * [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 @@ -819,9 +838,9 @@ 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? +# How to report bugs? -Please follow the instructions in [How do I report BLAST+ +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 From 46b5ef4f906c760874dd96b7e6783ae11ae9e4d7 Mon Sep 17 00:00:00 2001 From: Christiam Camacho Date: Tue, 7 Jul 2020 10:20:26 -0400 Subject: [PATCH 3/4] Simplify TOC --- README.md | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/README.md b/README.md index 4ef45a8..52671d7 100644 --- a/README.md +++ b/README.md @@ -11,21 +11,9 @@ This repository contains documentation for the [NCBI BLAST+](https://www.ncbi.nl * [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) * [Requirements](#requirements) * [Set up your GCP account and create a VM for analysis](#set-up-your-gcp-account-and-create-a-vm-for-analysis) - * [1. Creating your GCP account and registering for the free $300 credit program. (If you already have a GCP billing account, you can skip to step 2.)](#1-creating-your-gcp-account-and-registering-for-the-free-300-credit-program-if-you-already-have-a-gcp-billing-account-you-can-skip-to-step-2) - * [2. Create a Virtual Machine (VM)](#2-create-a-virtual-machine-vm) - * [3. Access a GCP VM from a local machine](#3-access-a-gcp-vm-from-a-local-machine) * [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) @@ -34,6 +22,7 @@ This repository contains documentation for the [NCBI BLAST+](https://www.ncbi.nl * [Commands to run](#commands-to-run) * [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) From cedb1bef925ec288be1d2fe5683ac2ce951d9227 Mon Sep 17 00:00:00 2001 From: Christiam Camacho Date: Tue, 7 Jul 2020 10:22:03 -0400 Subject: [PATCH 4/4] Simplify TOC --- README.md | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 52671d7..72f51a4 100644 --- a/README.md +++ b/README.md @@ -8,18 +8,9 @@ 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) - * [Requirements](#requirements) - * [Set up your GCP account and create a VM for analysis](#set-up-your-gcp-account-and-create-a-vm-for-analysis) - * [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) - * [Step 2. Import sequences and create a BLAST database](#step-2-import-sequences-and-create-a-blast-database) - * [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)