Mercurial > repos > mbernt > singularity_scriptrunner
comparison README.rst @ 0:9512201417a5 draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
| author | mbernt |
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| date | Sun, 06 Aug 2023 15:21:11 +0000 |
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| -1:000000000000 | 0:9512201417a5 |
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| 1 Note to admins: | |
| 2 =============== | |
| 3 | |
| 4 These tool allow users to execute arbitrary scripts in containers | |
| 5 (with singularity or apptainer). The interpreter (python, Rscript, | |
| 6 bash, ...) and the containers is configured by the admin using the | |
| 7 ``scripting_images`` data table. | |
| 8 | |
| 9 A basic level of security comes by the execution in containers. | |
| 10 Additional parameters that should be passed to the container engine | |
| 11 can be configured. | |
| 12 | |
| 13 Admins should consider the following points: | |
| 14 | |
| 15 - Passing the ``--cleanenv`` variable is certainy a good idea. | |
| 16 - The tool will mount the galaxy files dir for reading and only the | |
| 17 job working dir should be writable (might depend on your configuraion). | |
| 18 It's advisable to use the ``--no-mount`` option to disable additional | |
| 19 mounts that might be writable. | |
| 20 - Maybe disable or limit network usage, eg. for singularity ``--network none`` | |
| 21 | |
| 22 This tool has been inspired by the [scriptrunner](https://github.com/ARTbio/docker-scriptrunner/blob/master/scriptrunner.xml) tool | |
| 23 which works with docker. |