Mercurial > repos > mbernt > singularity_scriptrunner
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sun Aug 06 15:21:11 2023 +0000 @@ -0,0 +1,23 @@ +Note to admins: +=============== + +These tool allow users to execute arbitrary scripts in containers +(with singularity or apptainer). The interpreter (python, Rscript, +bash, ...) and the containers is configured by the admin using the +``scripting_images`` data table. + +A basic level of security comes by the execution in containers. +Additional parameters that should be passed to the container engine +can be configured. + +Admins should consider the following points: + +- Passing the ``--cleanenv`` variable is certainy a good idea. +- The tool will mount the galaxy files dir for reading and only the + job working dir should be writable (might depend on your configuraion). + It's advisable to use the ``--no-mount`` option to disable additional + mounts that might be writable. +- Maybe disable or limit network usage, eg. for singularity ``--network none`` + +This tool has been inspired by the [scriptrunner](https://github.com/ARTbio/docker-scriptrunner/blob/master/scriptrunner.xml) tool +which works with docker.