From 1a98582c2eb2d7abe8ab0012e62b2d8769e0470d Mon Sep 17 00:00:00 2001 From: Matthias Date: Thu, 6 Aug 2020 12:34:05 +0200 Subject: [PATCH] Update readme --- README.md | 38 ++++++++++++++++++++++++++++++++------ 1 file changed, 32 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index bf55906..3eb21f6 100644 --- a/README.md +++ b/README.md @@ -16,17 +16,43 @@ provides a comprehensive and intuitive user interface for the core functionalite ## More information There is a [Conda repository for openPrimeR available](https://anaconda.org/bioconda/bioconductor-openprimer/badges). -A [Docker container](https://hub.docker.com/r/mdoering88/openprimer/) for running openPrimeR/openPrimeRui is available. Usage: +For more information on how to install the third-party dependencies for openPrimeR, we refer to the corresponding [user-space repository](https://github.com/matdoering/openPrimeR-User), which provides installation routines. + +### Docker Instructions + +Our docker image is available at [dockerhub](https://hub.docker.com/r/mdoering88/openprimer/). In order to use the docker image, you need to [install docker](https://www.docker.com/) on your system and activate the docker daemon. + +After logging in with your docker account, in a console, enter + +>**docker pull mdoering88/openprimer** + +to retrieve the latest docker image of the tool. Since the image is quite large the download (~4 GB) may take some time, especially if your internet connection is not very fast. + +To run the image, enter + +>**docker run -p 3838:3838 --rm mdoering88/openprimer** + +After this, the tool is available by accessing **localhost:3838** in your web browser. + +In case you want to have more control of the image you are running or you want to study the output of the tool, you can execute + +>**docker run --rm -p 3838:3838 -v /tmp/logs/:/var/log/shiny-server/ mdoering88/openprimer:latest** + +With this call, the tool's log file is stored in the */tmp/logs/* folder on your system with a filename starting with *shiny-shiny*). During the session, you can use + +>**tail -f shiny-shiny-X.txt** + +to retrieve the current status messages. + +Moreover, in the above call to Docker, we have specified a tag, namely *:latest*, which means that we have started the most recent version of the tool. In case that no tag is provided, the latest available Docker image is used. + +You can also work with the openPrimeR API through the container by executing ``` -docker pull mdoering88/openprimer -# for openPrimeRui -docker run -rm -p 3838:3838 mdoering88/openprimer -# to work with openPrimeR via the CLI docker run -rm -it mdoering88/openprimer bash ``` -For more information on how to install openPrimeR, we refer to the corresponding [user-space repository](https://github.com/matdoering/openPrimeR-User), which provides installation routines. +and then starting an R session and loading the `openPrimeR` package. ## Changelog