From 310dd948f2ca6a8beee29ce802e465a98b9bd9b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 30 Jul 2024 20:11:54 +0200 Subject: [PATCH 1/2] make new jupyter notebook work --- files/galaxy/tpv/interactive_tools.yml | 3 +++ 1 file changed, 3 insertions(+) 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 From 36d53449a2f63a80b8b7a5696ed9c7456d855c9e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 30 Jul 2024 20:15:10 +0200 Subject: [PATCH 2/2] run qupath_roi_splitter in Docker --- files/galaxy/tpv/tools.yml | 2 ++ 1 file changed, 2 insertions(+) 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/.*: