Mercurial > repos > mbernt > singularity_scriptrunner

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 5c71b60920e887c5fdb2c0ca0118927b1231bde7
author mbernt
date Sun, 06 Aug 2023 16:01:26 +0000
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3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
parents:
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1 Note to admins:
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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2 ===============
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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4 These tool allow users to execute arbitrary scripts in containers
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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5 (with singularity or apptainer). The interpreter (python, Rscript,
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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6 bash, ...) and the containers is configured by the admin using the
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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7 ``scripting_images`` data table.
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
parents:
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3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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9 A basic level of security comes by the execution in containers.
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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10 Additional parameters that should be passed to the container engine
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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11 can be configured.
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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13 Admins should consider the following points:
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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15 - Passing the ``--cleanenv`` variable is certainy a good idea.
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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16 - The tool will mount the galaxy files dir for reading and only the
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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17 job working dir should be writable (might depend on your configuraion).
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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18 It's advisable to use the ``--no-mount`` option to disable additional
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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19 mounts that might be writable.
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
mbernt
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20 - Maybe disable or limit network usage, eg. for singularity ``--network none``
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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22 This tool has been inspired by the [scriptrunner](https://github.com/ARTbio/docker-scriptrunner/blob/master/scriptrunner.xml) tool
3d41fa089db7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
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23 which works with docker.