From 8b0a30b6f789ad6ba823ddd4003071f9be2dff7c Mon Sep 17 00:00:00 2001 From: clintval Date: Sun, 15 Dec 2024 19:18:18 -0500 Subject: [PATCH] chore: badges in README --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 8368d46..ccf7a2e 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![Java Version](https://img.shields.io/badge/java-11,17,21-c22d40.svg)](https://github.com/AdoptOpenJDK/homebrew-openjdk) [![Python Versions](https://img.shields.io/badge/python-3.11_|_3.12_|_3.13-blue)](https://github.com/clintval/typeline) -Tools for programmatically annotating VCFs with the Seshat TP53 database. +Tools for programmatically annotating VCFs with the [Seshat TP53 database](http://vps338341.ovh.net/). ![Mount Shuksan](.github/img/cover.jpg) @@ -20,7 +20,7 @@ Install with the Conda or Mamba package manager after setting your [Bioconda cha ## Quick Usage Example -For a round-trip annotation of a VCF file, execute a command like: +For round-trip Seshat annotation of a VCF file, execute a command like: ```bash ❯ seshat round-trip \ @@ -59,7 +59,7 @@ For a round-trip annotation of a VCF file, execute a command like: ## Upload a VCF to Seshat -Upload a VCF to the [Seshat TP53 annotation server](http://vps338341.ovh.net/) using a headless browser. +Upload a VCF to the Seshat annotation webserver using a headless browser. ```bash ❯ seshat upload-vcf \ @@ -109,7 +109,7 @@ Distributions of MacOS may require you to authenticate the Chrome driver ([link] ## Download a Seshat Annotation from Gmail -Download [Seshat](http://vps338341.ovh.net/) VCF annotations by awaiting a server-generated email. +Download Seshat VCF annotations by awaiting a server-generated email. ```bash ❯ seshat find-in-gmail \ @@ -213,7 +213,7 @@ If Seshat fails to annotate the VCF file but still emails the user a response, t ## Merge Annotations into a VCF -Merge annotations into the `INFO` fields of the VCF. +Merge Seshat annotations into the `INFO` fields of the VCF. ```bash ❯ seshat merge \