From e629a9d44dede7324ac3c59c74760f3729e4b97a Mon Sep 17 00:00:00 2001 From: Oliver Schwengers Date: Mon, 10 Feb 2020 14:46:59 +0100 Subject: [PATCH 1/4] polish readme --- README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 6044efc..b21fcc6 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,11 @@ ## Contents - [Description](#description) - [Features](#features) + - [Per Isolate](#per-isolate) + - [Comparative](#comparative) - [Availability](#availability) + - [Docker](#docker) + - [Cloud](#cloud-openstack) - [Input/Output](#inputoutput) - [Citation](#citation) - [License](#license) @@ -132,7 +136,7 @@ $ asap/asap-docker.sh -p example-lmonocytogenes-4/ For further information have a look at the Docker readme (docker/DOCKER.md ). -### Cloud - OpenStack +### Cloud OpenStack ASA³P's **OpenStack** based cloud version targets the analysis of hundreds to even thousands of bacterial isolates. Therefore, it features automatic creation, setup and orchestration of an **SGE** based compute cluster and its entire From 1ebd6b25d805521ad8c27e6eab896ed6fcf19df9 Mon Sep 17 00:00:00 2001 From: Oliver Schwengers Date: Mon, 10 Feb 2020 14:51:24 +0100 Subject: [PATCH 2/4] Update preliminary citation --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index b21fcc6..2e562c3 100644 --- a/README.md +++ b/README.md @@ -330,6 +330,10 @@ project-dir To cite our work, please transitionally refer to: +> Schwengers et al. (in press). ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher level analysis of closely related bacterial isolates. PLOS Computational Biology + +Alternatively, you can also cite our bioRxiv preprint: + > ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher level analysis of closely related bacterial isolates. Oliver Schwengers, Andreas Hoek, Moritz Fritzenwanker, Linda Falgenhauer, Torsten Hain, Trinad Chakraborty, Alexander Goesmann. bioRxiv 654319; doi: https://doi.org/10.1101/654319 ## License From a20016df482f7f62b6dd2c4901f46c92074a5a39 Mon Sep 17 00:00:00 2001 From: Sebastian Jaenicke Date: Wed, 19 Feb 2020 13:31:40 +0100 Subject: [PATCH 3/4] fix typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 2e562c3..0fe0b91 100644 --- a/README.md +++ b/README.md @@ -344,7 +344,7 @@ A file (README.md) within the ASA³P directory contains a list of all dependencies and related licenses. **NOTE** -Please, notice that some bundled dependecies are published under a +Please, notice that some bundled dependencies are published under a **free-for-academic** or **free-for-non-commercial** usage license model. To our best knowledge this is true for at least the following databases: - CARD: free for academic usage From 9cdc9304a00a9efe55fa41eb0bb4a0cf897706cf Mon Sep 17 00:00:00 2001 From: Oliver Schwengers Date: Fri, 6 Mar 2020 14:46:01 +0100 Subject: [PATCH 4/4] update citation --- README.md | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 0fe0b91..b1d65e0 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![DOI:10.1101/654319v1](https://zenodo.org/badge/DOI/10.1101/654319.svg)](https://www.biorxiv.org/content/10.1101/654319v1) +[![DOI:10.1371/journal.pcbi.1007134](https://zenodo.org/badge/DOI/10.1371/journal.pcbi.1007134.svg)](https://doi.org/10.1371/journal.pcbi.1007134) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/oschwengers/asap/blob/master/LICENSE) ![Don't judge me](https://img.shields.io/badge/Language-Groovy-blue.svg) ![GitHub release](https://img.shields.io/github/release/oschwengers/asap.svg) @@ -328,13 +328,7 @@ project-dir ## Citation -To cite our work, please transitionally refer to: - -> Schwengers et al. (in press). ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher level analysis of closely related bacterial isolates. PLOS Computational Biology - -Alternatively, you can also cite our bioRxiv preprint: - -> ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher level analysis of closely related bacterial isolates. Oliver Schwengers, Andreas Hoek, Moritz Fritzenwanker, Linda Falgenhauer, Torsten Hain, Trinad Chakraborty, Alexander Goesmann. bioRxiv 654319; doi: https://doi.org/10.1101/654319 +> Schwengers et al. (2020). ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher level analysis of closely related bacterial isolates. PLOS Computational Biology 16(3): e1007134. https://doi.org/10.1371/journal.pcbi.1007134 ## License ASA³P itself is published and distributed under GPL3 license. In contradiction,