# HG changeset patch
# User mbernt
# Date 1691335271 0
# Node ID 9512201417a58467dd5cc65d9b7b01afa37ed793
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 9e9a0860d255a1fd6c43edd0fde9ea538ee679de
diff -r 000000000000 -r 9512201417a5 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Sun Aug 06 15:21:11 2023 +0000
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+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.
diff -r 000000000000 -r 9512201417a5 general.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/general.xml Sun Aug 06 15:21:11 2023 +0000
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diff -r 000000000000 -r 9512201417a5 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sun Aug 06 15:21:11 2023 +0000
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\ No newline at end of file
diff -r 000000000000 -r 9512201417a5 test-data/scripting_images.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scripting_images.loc Sun Aug 06 15:21:11 2023 +0000
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+#
+
+# docker://continuumio/anaconda3
+python_continuumio_anaconda python (continuumio/anaconda) /tmp/anaconda3_latest.sif python singularity --cleanenv --network none --no-mount bind-paths
+
+# docker://rocker/tidyverse
+r_rocker_tidyverse R (tidyverse) /tmp/tidyverse_latest.sif Rscript apptainer
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+# docker://rocker/tidyverse
+bash_continuumio_anaconda bash (continuumio/anaconda) /tmp/anaconda3_latest.sif bash apptainer --cleanenv --network none --no-mount bind-paths
\ No newline at end of file
diff -r 000000000000 -r 9512201417a5 test-data/test.feather
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diff -r 000000000000 -r 9512201417a5 test-data/test.h5
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diff -r 000000000000 -r 9512201417a5 test-data/test.rds
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diff -r 000000000000 -r 9512201417a5 test-data/test.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.tsv Sun Aug 06 15:21:11 2023 +0000
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+A B
+1 2
+2 1
diff -r 000000000000 -r 9512201417a5 tool-data/scripting_images.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/scripting_images.loc Sun Aug 06 15:21:11 2023 +0000
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+# the following six tab separated columns need to be set
+#
+# id
+# a unique id to be used
+# name
+# name shown to the user
+# image_name
+# a path or URL to an image to use. Note that when using URLs
+# it images will be pulled on the fly to the job working dir
+# and the user executing the tools needs to take care of the
+# image cache.
+# interpreter
+# the interpreter that should be applied to the user supplied scripts
+# container_type
+# apptainer/singularity
+# container_params
+# parameters to be passed to singularity/apptainer
+# --cleanenv --network none --no-mount bind-paths --cpus "\${GALAXY_SLOTS:-1}"
+#
+# \t\t\t\t\t
diff -r 000000000000 -r 9512201417a5 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Sun Aug 06 15:21:11 2023 +0000
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+ value, name, image, interpreter, container_type, container_params
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diff -r 000000000000 -r 9512201417a5 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Sun Aug 06 15:21:11 2023 +0000
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+
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+ value, name, image, interpreter, container_type, container_params
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+
\ No newline at end of file