From 79c2ec6acfc09123eed629d62ba7b64191be3807 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micha=C5=82=20Szczepanik?= Date: Tue, 9 Sep 2025 18:11:30 +0200 Subject: [PATCH] Prevent apptainer from mounting user's home directory Disabling the mount of $HOME may, in particular, prevent clashes with Python library files being present in user's $HOME. This is less restrictive than `--containall` but should be sufficient. Closes #1 https://apptainer.org/docs/user/main/bind_paths_and_mounts.html#using-no-home-and-containall-flags --- .datalad/config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.datalad/config b/.datalad/config index 945c2e7..3c22c7f 100644 --- a/.datalad/config +++ b/.datalad/config @@ -5,4 +5,4 @@ cmdexec = {python} -m datalad_container.adapters.docker run {img} {cmd} [datalad "containers.apptainer"] image = apptainer/nipy-heudiconv--1.3.3.sing - cmdexec = apptainer exec {img} bash -c 'PATH=/opt/dcm2niix-v1.0.20240202/bin:$PATH /opt/miniconda-py39_4.12.0/bin/heudiconv {cmd}' + cmdexec = apptainer exec --no-home {img} bash -c 'PATH=/opt/dcm2niix-v1.0.20240202/bin:$PATH /opt/miniconda-py39_4.12.0/bin/heudiconv {cmd}' -- 2.52.0