A startup.sh script, that is usually starting Apache, PostgreSQL and Galaxy, will recognize the export directory with one of the following outcomes: Given the additional -v /home/user/galaxy_storage/:/export/ parameter, docker will mount the folder /home/user/galaxy_storage into the Container under /export/. $ docker run -d -p 8080:80 -v /home/user/galaxy_storage/:/export/ quay.io/bgruening/galaxy-rna-workbench
#Kitematic inverse how to#
The following video shows how to load the docker container that is necessary to use the workbench:įor non-Kitematic users, starting the RNA workbench is analogous to start the generic Galaxy Docker image: Kitematic users can launch the RNA workbench directly from its interface. Whether you run Docker images using Kitematic or the command line interface, the procedure to launch the RNA workbench varies. So for users new to docker, we list here some tweaks that can help to work around issues when first using docker.Īfter successful installation of docker, it is recommended to configure some settings, dealing for example with the storage space required by containers. The RNA workbench docker container is rather large and expected to grow when further tools and workflows are contributed. linux users and people familiar with the command line can follow the instruction on installing Docker from its website.non-linux users are encouraged to use Kitematic, which provides a Docker installation for OSX or Windows, coupled with a user friendly interface to run Docker containers.To use the Galaxy RNA workbench, you only need Docker, which can be installed in different ways, depending on the type of system you’re running: The workbench is directly use and testable as instance of. For advanced local deployments, we recommend to check out the upstream documentation. The RNA analyses workbench implements a webserver based on the Galaxy Docker platform: a dedicated Galaxy instance wrapped in a Docker container.
This center is one of the eight service units of the German Network for Bioinformatics Infrastructure, running the German ELIXIR Node. The workbench is developed by the RNA Bioinformatics Center (RBC).
The current implementation comprises more than 50 bioinformatics tools dedicated to different research areas of RNA biology, including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-Seq analysis, and RNA target prediction. The workbench is described in two manuscripts published in Nucleic Acid Research (see version1, version2). The workbench is based on the Galaxy framework, which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge. The RNA Galaxy workbench is a comprehensive set of analysis tools and consolidated workflows.
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