FIX add default header and entrypoint to docker and singularity files

ReproNim · Jun 22, 2024 · 6f3eb4b · 6f3eb4b
1 parent e4a3eed
commit 6f3eb4b
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Showing 2 changed files with 18 additions and 8 deletions.
diff --git a/neurodocker/cli/generate.py b/neurodocker/cli/generate.py
@@ -327,6 +327,16 @@ def _params_to_renderer_dict(ctx: click.Context, pkg_manager) -> dict:
             renderer_dict["instructions"].append(d)
     if not renderer_dict["instructions"]:
         ctx.fail("not enough instructions to generate a container specification")
+    # Add header to the instructions, after the base image.
+    renderer_dict["instructions"].insert(
+        1, {"name": "_default", "kwds": {}}
+    )
+    # Use default entrypoint if user did not specify one.
+    if "entrypoint" not in [param.name for param, _ in cmd._options]:
+        renderer_dict["instructions"].append(
+            {"name": "entrypoint", "kwds": {"args": ["/neurodocker/startup.sh"]}}
+        )
+
     return renderer_dict
 
 

diff --git a/neurodocker/templates/_header.yaml → neurodocker/templates/_default.yaml b/neurodocker/templates/_header.yaml → neurodocker/templates/_default.yaml
@@ -4,7 +4,7 @@
 
 # TODO: read this about locales http://jaredmarkell.com/docker-and-locales/
 
-name: _header
+name: _default
 url: n/a
 # Not actually source, but we do not want to provide URLs.
 source:
@@ -28,14 +28,14 @@ source:
         LC_ALL: en_US.UTF-8
         ND_ENTRYPOINT: /neurodocker/startup.sh
     instructions: |
-        export ND_ENTRYPOINT="{{ _header._env['ND_ENTRYPOINT'] }}"
-        {{ _header.install_dependencies() }}
-        {%- if _header.pkg_manager == "apt" %}
-        sed -i -e 's/# {{ _header._env['LC_ALL'] }} UTF-8/{{ _header._env['LC_ALL'] }} UTF-8/' /etc/locale.gen
+        export ND_ENTRYPOINT="{{ self.env['ND_ENTRYPOINT'] }}"
+        {{ self.install_dependencies() }}
+        {%- if self.pkg_manager == "apt" %}
+        sed -i -e 's/# {{ self.env['LC_ALL'] }} UTF-8/{{ self.env['LC_ALL'] }} UTF-8/' /etc/locale.gen
         dpkg-reconfigure --frontend=noninteractive locales
-        update-locale LANG="{{ _header._env['LANG'] }}"
-        {%- elif _header.pkg_manager == "yum" %}
-        localedef -i {{ _header._env['LC_ALL'].split('.')[0] }} -f {{ _header._env['LC_ALL'].split('.')[1] }} {{ _header._env['LC_ALL'] }}
+        update-locale LANG="{{ self.env['LANG'] }}"
+        {%- elif self.pkg_manager == "yum" %}
+        localedef -i {{ self.env['LC_ALL'].split('.')[0] }} -f {{ self.env['LC_ALL'].split('.')[1] }} {{ self.env['LC_ALL'] }}
         {%- endif %}
         chmod 777 /opt && chmod a+s /opt
         mkdir -p /neurodocker