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planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
author mvdbeek
date Sun, 22 Jul 2018 13:37:34 -0400
parents cf6e2bba9714
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13:cf6e2bba9714 14:5a3652633289
1 [![Build Status](https://travis-ci.org/ARTbio/docker-scriptrunner.svg?branch=master)](https://travis-ci.org/ARTbio/docker-scriptrunner)
2
3 You need to have docker
1 Docker scriptrunner for galaxy 4 Docker scriptrunner for galaxy
2 ----------------------------- 5 -----------------------------
3 6
4 This is a [galaxy](https://github.com/galaxyproject/galaxy) tool that allows 7 This is a [galaxy](https://github.com/galaxyproject/galaxy) tool that allows
5 users to submit random scripts. 8 users to submit random scripts.
9 You can install it on your galaxy server from the [galaxy toolshed] (https://toolshed.g2.bx.psu.edu/view/mvdbeek/docker_scriptrunner/).
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12 This tool is heavily inspired by Ross Lazarus' tool factory
13 (https://www.ncbi.nlm.nih.gov/pubmed/23024011), but removes the ability to
14 create galaxy tools. (If you are looking at creating galaxy tools, you may want
15 to use [planemo](https://planemo.readthedocs.io/en/latest/)).
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18 You need to have docker installed on any machine that can run
19 galaxy jobs, or route this tool to a dedicated docker host
20 in galaxy's job_conf.xml. Note that the tool itself talks
21 to the docker daemon and bypasses galaxy's docker configuration.
22 Making use of galaxy's docker capabilities is on the roadmap.
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25 The tool comes with two docker images that can be easily extended.
26 "artbio/scriptrunner" is a base image, that has very few dependencies installed.
27 You can extend the image by following the example in the dockerfiles/r-bioperl-python
28 folder.
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31 All security relies on docker; the container only mounts those files that the user
32 has selected as input files, and the script itself drops privileged inside
33 the container. This should be secure, but caution should be taken on public servers.
34 By default the container has networking enabled, so make sure your firewall rules
35 forbid traffic to the local network.