Mercurial > repos > mvdbeek > docker_scriptrunner
diff README.md @ 2:495946ffc2d6 draft default tip
planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
| author | mvdbeek |
|---|---|
| date | Sun, 22 Jul 2018 13:38:01 -0400 |
| parents | 21d312776891 |
| children |
line wrap: on
line diff
--- a/README.md Sat Jul 09 17:00:06 2016 -0400 +++ b/README.md Sun Jul 22 13:38:01 2018 -0400 @@ -1,6 +1,35 @@ +[](https://travis-ci.org/ARTbio/docker-scriptrunner) + +You need to have docker Docker scriptrunner for galaxy ----------------------------- This is a [galaxy](https://github.com/galaxyproject/galaxy) tool that allows users to submit random scripts. -You can install it on your galaxy server from the [galaxy toolshed]() +You can install it on your galaxy server from the [galaxy toolshed] (https://toolshed.g2.bx.psu.edu/view/mvdbeek/docker_scriptrunner/). + + +This tool is heavily inspired by Ross Lazarus' tool factory +(https://www.ncbi.nlm.nih.gov/pubmed/23024011), but removes the ability to +create galaxy tools. (If you are looking at creating galaxy tools, you may want +to use [planemo](https://planemo.readthedocs.io/en/latest/)). + + +You need to have docker installed on any machine that can run +galaxy jobs, or route this tool to a dedicated docker host +in galaxy's job_conf.xml. Note that the tool itself talks +to the docker daemon and bypasses galaxy's docker configuration. +Making use of galaxy's docker capabilities is on the roadmap. + + +The tool comes with two docker images that can be easily extended. +"artbio/scriptrunner" is a base image, that has very few dependencies installed. +You can extend the image by following the example in the dockerfiles/r-bioperl-python +folder. + + +All security relies on docker; the container only mounts those files that the user +has selected as input files, and the script itself drops privileged inside +the container. This should be secure, but caution should be taken on public servers. +By default the container has networking enabled, so make sure your firewall rules +forbid traffic to the local network.