update base image of sct

NeuroDesk · Sep 25, 2024 · 21cb46d · 21cb46d
1 parent 3fdbc56
commit 21cb46d
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diff --git a/recipes/spinalcordtoolbox/README.md b/recipes/spinalcordtoolbox/README.md
@@ -1,6 +1,6 @@
 
 ----------------------------------
-## spinalcordtoolbox/6.4 ##
+## spinalcordtoolbox/toolVersion ##
 CT tools process MRI data (NIfTI files) and can do fully automatic tasks such as:
 - Segmentation of the spinal cord and gray matter
 - Segmentation of pathologies (eg. multiple sclerosis lesions)
@@ -20,7 +20,9 @@ SCT also has low-level tools:
 
 More documentation can be found here: https://spinalcordtoolbox.com/en/latest/user_section/getting-started.html
 
-To run container outside of this environment: ml spinalcordtoolbox/6.4
+To run container outside of this environment: ml spinalcordtoolbox/toolVersion
+
+license: LGPLv3 (https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/master/LICENSE)
 
 ----------------------------------
 
diff --git a/recipes/spinalcordtoolbox/build.sh b/recipes/spinalcordtoolbox/build.sh
@@ -12,7 +12,7 @@ fi
 source ../main_setup.sh
 
 neurodocker generate ${neurodocker_buildMode} \
-   --base-image ubuntu:16.04 \
+   --base-image ubuntu:20.04 \
    --pkg-manager apt \
    --install="gcc ca-certificates libmpich-dev python3-pyqt5 git curl bzip2 libglib2.0-0 rsync" \
    --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
@@ -21,7 +21,6 @@ neurodocker generate ${neurodocker_buildMode} \
    --run="curl -fsSL --retry 5 https://github.com/spinalcordtoolbox/spinalcordtoolbox/archive/refs/tags/${toolVersion}.tar.gz | tar -xz -C /opt/ " \
    --workdir="/opt/${toolName}-${toolVersion}" \
    --run="chmod a+rwx /opt/${toolName}-${toolVersion}/ -R" \
-   --run="curl https://raw.githubusercontent.com/NeuroDesk/neurocontainers/master/recipes/spinalcordtoolbox/README.md -o /README.md" \
    --user=${toolName} \
    --run="yes | ./install_sct -i" \
    --env DEPLOY_PATH=/opt/${toolName}-${toolVersion}/bin/ \
@@ -34,6 +33,7 @@ neurodocker generate ${neurodocker_buildMode} \
    --run="sct_deepseg -install-task seg_mice_sc" \
    --run="sct_deepseg -install-task seg_sc_t2star" \
    --run="bash /opt/spinalcordtoolbox-${toolVersion}/batch_processing.sh" \
+   --copy README.md /README.md \
   > ${toolName}_${toolVersion}.Dockerfile