diff --git a/files/galaxy/tpv/interactive_tools.yml b/files/galaxy/tpv/interactive_tools.yml index dd29a20eb..6143c51fc 100644 --- a/files/galaxy/tpv/interactive_tools.yml +++ b/files/galaxy/tpv/interactive_tools.yml @@ -244,6 +244,9 @@ tools: interactive_tool_jupyter_notebook: inherits: interactive_tool mem: 4 + params: + # needed for > quay.io/bgruening/docker-jupyter-notebook:24.07, this image starts as root but drops privileges + docker_run_extra_arguments: "-e NB_UID=999" env: HOME: /home/jovyan diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 3cde3e8fc..de3b13ef4 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -331,6 +331,8 @@ tools: _GALAXY_JOB_TMP_DIR: '/tmp' toolshed.g2.bx.psu.edu/repos/goeckslab/gate_finder/gate_finder/.*: inherits: basic_docker_tool + toolshed.g2.bx.psu.edu/repos/galaxyp/qupath_roi_splitter/qupath_roi_splitter/.*: + inherits: basic_docker_tool toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/.*: inherits: basic_docker_tool toolshed.g2.bx.psu.edu/repos/bgruening/cellpose/cellpose/.*: