Use conda

bids-apps · Jun 26, 2020 · 6d40956 · 6d40956
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commit 6d40956
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diff --git a/Dockerfile b/Dockerfile
@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.4.2-3-gf7055a1
-# Timestamp: 2020-06-25 20:45:40 UTC
+# Timestamp: 2020-06-26 19:59:46 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -48,11 +48,6 @@ RUN apt-get update -qq \
            perl-modules \
            wget \
            curl \
-           python3 \
-           python3-pip \
-           python3-pandas \
-           python-pip \
-           python3-setuptools \
            libsm-dev \
            libx11-dev \
            libxt-dev \
@@ -92,7 +87,31 @@ RUN apt-get update -qq \
          --exclude='freesurfer/trctrain' \
     && sed -i '$isource "/opt/freesurfer/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"
 
-RUN bash -c 'pip3 install nibabel pandas==0.21.0'
+ENV CONDA_DIR="/opt/miniconda-latest" \
+    PATH="/opt/miniconda-latest/bin:$PATH"
+RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
+    && echo "Downloading Miniconda installer ..." \
+    && conda_installer="/tmp/miniconda.sh" \
+    && curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && bash "$conda_installer" -b -p /opt/miniconda-latest \
+    && rm -f "$conda_installer" \
+    && conda update -yq -nbase conda \
+    && conda config --system --prepend channels conda-forge \
+    && conda config --system --set auto_update_conda false \
+    && conda config --system --set show_channel_urls true \
+    && sync && conda clean -tipsy && sync \
+    && conda install -y -q --name base \
+           'python=3' \
+           'pip' \
+           'pandas' \
+           'setuptools' \
+           'pandas=0.21.0' \
+    && sync && conda clean -tipsy && sync \
+    && bash -c "source activate base \
+    &&   pip install --no-cache-dir  \
+             'nibabel'" \
+    && rm -rf ~/.cache/pip/* \
+    && sync
 
 RUN bash -c 'curl -sL https://deb.nodesource.com/setup_6.x | bash -'
 
@@ -163,11 +182,6 @@ RUN echo '{ \
     \n        "perl-modules", \
     \n        "wget", \
     \n        "curl", \
-    \n        "python3", \
-    \n        "python3-pip", \
-    \n        "python3-pandas", \
-    \n        "python-pip", \
-    \n        "python3-setuptools", \
     \n        "libsm-dev", \
     \n        "libx11-dev", \
     \n        "libxt-dev", \
@@ -183,8 +197,20 @@ RUN echo '{ \
     \n      } \
     \n    ], \
     \n    [ \
-    \n      "run_bash", \
-    \n      "pip3 install nibabel pandas==0.21.0" \
+    \n      "miniconda", \
+    \n      { \
+    \n        "use_env": "base", \
+    \n        "conda_install": [ \
+    \n          "python=3", \
+    \n          "pip", \
+    \n          "pandas", \
+    \n          "setuptools", \
+    \n          "pandas=0.21.0" \
+    \n        ], \
+    \n        "pip_install": [ \
+    \n          "nibabel" \
+    \n        ] \
+    \n      } \
     \n    ], \
     \n    [ \
     \n      "run_bash", \

diff --git a/Singularity b/Singularity
@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.4.2-3-gf7055a1
-# Timestamp: 2020-06-25 20:45:41 UTC
+# Timestamp: 2020-06-26 19:59:47 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or

diff --git a/generate_freesurfer_images.sh b/generate_freesurfer_images.sh
@@ -46,10 +46,9 @@ docker run --rm ${image} generate docker \
   --base ubuntu:xenial \
   --pkg-manager apt \
   --install tcsh bc tar libgomp1 perl-modules wget curl \
-    python3 python3-pip python3-pandas python-pip python3-setuptools \
     libsm-dev libx11-dev libxt-dev libxext-dev libglu1-mesa \
   --freesurfer version=6.0.1 install_path=/opt/freesurfer \
-  --run-bash 'pip3 install nibabel pandas==0.21.0' \
+  --miniconda use_env=base conda_install="python=3 pip pandas setuptools pandas=0.21.0" pip_install="nibabel" \
   --run-bash 'curl -sL https://deb.nodesource.com/setup_6.x | bash -' \
   --install nodejs \
   --run-bash 'npm install -g [email protected]' \
@@ -80,10 +79,9 @@ docker run --rm ${image} generate singularity \
   --base ubuntu:xenial \
   --pkg-manager apt \
   --install tcsh bc tar libgomp1 perl-modules wget curl \
-    python3 python3-pip python3-pandas python-pip python3-setuptools \
     libsm-dev libx11-dev libxt-dev libxext-dev libglu1-mesa \
   --freesurfer version=6.0.1 install_path=/opt/freesurfer \
-  --run-bash 'pip3 install nibabel pandas==0.21.0' \
+  --miniconda use_env=base conda_install="python=3 pip pandas setuptools pandas=0.21.0" pip_install="nibabel" \
   --run-bash 'curl -sL https://deb.nodesource.com/setup_6.x | bash -' \
   --install nodejs \
   --run-bash 'npm install -g [email protected]' \