diff --git a/README.md b/README.md index b2b55d9..c81f9ab 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,17 @@ # mtDNA-Server 2 + [![mtdna-server-2](https://github.com/genepi/mtdna-server-2/actions/workflows/run-tests.yml/badge.svg)](https://github.com/genepi/mtdna-server-2/actions/workflows/run-tests.yml) [![nf-test](https://img.shields.io/badge/tested_with-nf--test-337ab7.svg)](https://github.com/askimed/nf-test) -Welcome to mtdna-Server 2. This repository includes the mtDNA-Server-2 Workflow ported to Nextflow. +Welcome to mtdna-Server 2. This repository includes the mtDNA-Server-2 Workflow ported to Nextflow. ## Access -mtDNA-Server 2 is hosted as a service on our [mitoverse](https://mitoverse.i-med.ac.at/) platform. +mtDNA-Server 2 is hosted as a service on our [mitoverse](https://mitoverse.i-med.ac.at/) platform. ## Documentation -Documentation can be accessed [here](https://mitoverse.readthedocs.io). + +Documentation can be accessed [here](https://mitoverse.readthedocs.io/mtdna-server/mtdna-server/). ## Local Installation @@ -17,15 +19,25 @@ Documentation can be accessed [here](https://mitoverse.readthedocs.io). #### Requirements +- Docker or Singularity +- Java 14 - Nextflow: + ``` curl -s https://get.nextflow.io | bash ``` -#### Execution +#### Installation + +Build Docker image: ``` docker build -t genepi/mtdna-server-2 . # don't ingore the dot here +``` + +#### Execution + +``` nextflow run main.nf -c tests/test_single_bam.config -profile development ``` @@ -40,18 +52,26 @@ nextflow run main.nf -c tests/test_single_bam.config -profile development #### Installation - Install cloudgene3: `curl -s install.cloudgene.io | bash -s 3.0.0-beta4` -- Download latest source code zip file from releases - Install mtDNA-Server 2 workflow: `./cloudgene install https://github.com/genepi/mtdna-server-2/archive/refs/tags/v2.0.0-beta2.zip` - Start cloudgene server: `./cloudgene server` - Open [http://localhost:8082](http://localhost:8082) - Login with default admin account: username `admin` and password `admin1978` -- mtDNA-Server-2 can be tested with the following [test file](https://github.com/genepi/mtdna-server-2/raw/main/tests/data/bam/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam)) +- mtDNA-Server-2 can be tested with the following [test file](https://github.com/genepi/mtdna-server-2/raw/main/tests/data/bam/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam) ## Publication + Weissensteiner H*, Forer L*, Fuchsberger C, Schöpf B, Kloss-Brandstätter A, Specht G, Kronenberg F, Schönherr S: mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud. Nucleic Acids Res. 44:W64-9, 2016. PMID: [27084948](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987870/) ## Contact -Institute of Genetic Epidemiology, Medical University of Innsbruck + +This software was developed at the [Institute of Genetic Epidemiology](https://genepi.i-med.ac.at/), [Medical University of Innsbruck](https://i-med.ac.at/) + +![](https://avatars2.githubusercontent.com/u/1942824?s=30) [Sebastian Schoenherr](mailto:sebastian.schoenherr@i-med.ac.at) ([@seppinho](https://twitter.com/seppinho)) + +![](https://avatars2.githubusercontent.com/u/1931865?s=30) [Hansi Weissensteiner](mailto:hansi.weissensteiner@i-med.ac.at) ([@whansi](https://twitter.com/whansi)) + +![](https://avatars2.githubusercontent.com/u/210220?s=30) [Lukas Forer](mailto:lukas.forer@i-med.ac.at) ([@lukfor](https://twitter.com/lukfor)) ## License + MIT Licensed.