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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
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5a3652633289 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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1 [![Build Status](https://travis-ci.org/ARTbio/docker-scriptrunner.svg?branch=master)](https://travis-ci.org/ARTbio/docker-scriptrunner)
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5a3652633289 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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3 You need to have docker
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4 Docker scriptrunner for galaxy
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5 -----------------------------
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7 This is a [galaxy](https://github.com/galaxyproject/galaxy) tool that allows
cf6e2bba9714 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1
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8 users to submit random scripts.
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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
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13 (https://www.ncbi.nlm.nih.gov/pubmed/23024011), but removes the ability to
5a3652633289 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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14 create galaxy tools. (If you are looking at creating galaxy tools, you may want
5a3652633289 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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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
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19 galaxy jobs, or route this tool to a dedicated docker host
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20 in galaxy's job_conf.xml. Note that the tool itself talks
5a3652633289 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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21 to the docker daemon and bypasses galaxy's docker configuration.
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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.
5a3652633289 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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26 "artbio/scriptrunner" is a base image, that has very few dependencies installed.
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27 You can extend the image by following the example in the dockerfiles/r-bioperl-python
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28 folder.
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31 All security relies on docker; the container only mounts those files that the user
5a3652633289 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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32 has selected as input files, and the script itself drops privileged inside
5a3652633289 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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33 the container. This should be secure, but caution should be taken on public servers.
5a3652633289 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
mvdbeek
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34 By default the container has networking enabled, so make sure your firewall rules
5a3652633289 planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit dded837d19aeb3f06b84e5076282cedeeaf713fa
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35 forbid traffic to the local network.