From 89418cc186e6f50bd9c7c16d55c56c22d32159b3 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Sat, 22 Jun 2024 12:06:52 -0700 Subject: [PATCH 1/2] FIX strip-components 2 for freesurfer 7.4.1 --- neurodocker/templates/freesurfer.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/neurodocker/templates/freesurfer.yaml b/neurodocker/templates/freesurfer.yaml index 9c2ee47b..97464da2 100644 --- a/neurodocker/templates/freesurfer.yaml +++ b/neurodocker/templates/freesurfer.yaml @@ -84,7 +84,7 @@ binaries: echo "Downloading FreeSurfer ..." mkdir -p {{ self.install_path }} curl -fL {{ self.urls[self.version] }} \ - | tar -xz -C {{ self.install_path }} --owner root --group root --no-same-owner --strip-components 1 {% if self.exclude_paths -%}\ + | tar -xz -C {{ self.install_path }} --owner root --group root --no-same-owner --strip-components {% if self.version in ("7.4.1") %}2{% else %}1{% endif %} {% if self.exclude_paths -%}\ {%- for exclude_path in self.exclude_paths.split() %} {% if not loop.last -%} --exclude='{{ exclude_path }}' \ From 2dc1f11cc8d6131e89fccbebc11f086d02f1782f Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Fri, 5 Jul 2024 15:51:37 -0700 Subject: [PATCH 2/2] Use --transform instead of --strip-components --- neurodocker/templates/freesurfer.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/neurodocker/templates/freesurfer.yaml b/neurodocker/templates/freesurfer.yaml index 97464da2..6f0167f0 100644 --- a/neurodocker/templates/freesurfer.yaml +++ b/neurodocker/templates/freesurfer.yaml @@ -84,7 +84,7 @@ binaries: echo "Downloading FreeSurfer ..." mkdir -p {{ self.install_path }} curl -fL {{ self.urls[self.version] }} \ - | tar -xz -C {{ self.install_path }} --owner root --group root --no-same-owner --strip-components {% if self.version in ("7.4.1") %}2{% else %}1{% endif %} {% if self.exclude_paths -%}\ + | tar -xz -C {{ self.install_path }} --owner root --group root --no-same-owner --transform='s,freesurfer/,,' {% if self.exclude_paths -%}\ {%- for exclude_path in self.exclude_paths.split() %} {% if not loop.last -%} --exclude='{{ exclude_path }}' \