From 3695ab56c2ccef6b55c30add1ae4a881efd1f10a Mon Sep 17 00:00:00 2001 From: Oliver-Lorenz-dev Date: Thu, 5 Sep 2024 15:22:59 +0100 Subject: [PATCH] add docker instructions --- README.md | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 707b63f..cde16a9 100644 --- a/README.md +++ b/README.md @@ -11,11 +11,13 @@ SeroBA is a k-mer based Pipeline to identify the Serotype from Illumina NGS read - [Introduction](#introduction) - [Docker Image](#docker-image) - [Usage](#usage) + - [Running with docker](#running-with-docker) + - [Running with singularity](#running-with-singularity) - [Running the tests](#running-the-tests) - [Setting up the database](#setting-up-the-database) - [Creates a Database for kmc and ariba](#creates-a-database-for-kmc-and-ariba) - [Identify serotype of your input data](#identify-serotype-of-your-input-data) - - [Summaries the output in one tsv file](#summaries-the-output-in-one-tsv-file) + - [Summarise the output in one csv file](#summarises-the-output-in-one-csv-file) - [Output](#output) - [Troubleshooting](#troubleshooting) - [License](#license) @@ -31,6 +33,17 @@ Upon each release, a Docker Image is automatically built and pushed to [Docker H ## Usage All the following instructions are assuming you are working within a Docker container +### Running with docker +To run serotyping with docker using the pre-built docker image which contains the database, run a command like this (replacing /path/to/reads with the folder containing your reads and /data/read_[12].fastq.gz with your read files) + +```docker run --rm -it -v /path/to/reads:/data sangerbentleygroup/seroba seroba runSerotyping /seroba/database /data/read_1.fastq.gz /data/read_2.fastq.gz /data/output_folder``` + +### Running with singularity +To run serotyping with singularity using the pre-built docker image which contains the database, run a command like this (replacing /path/to/reads with the folder containing your reads and /data/read_[12].fastq.gz with your read files) + +```singularity exec --bind /path/to/reads:/data docker://sangerbentleygroup/seroba seroba runSerotyping /seroba/database /data/read_1.fastq.gz /data/read_2.fastq.gz /data/output_folder``` + + ### Running the tests The test can be run from the top level directory: @@ -71,7 +84,7 @@ usage: seroba runSerotyping [options]