organize profile settings #1536

Author: oesteban

docker/test-image-base/Dockerfile

@@ -74,11 +74,11 @@ RUN curl -sSL http://neuro.debian.net/lists/vivid.de-m.full | tee /etc/apt/sourc
     apt-get update && \
     apt-get install -y fsl-core afni
 
-RUN echo '#!/bin/bash' > /etc/profile.d/nipype.sh && \
-    echo 'export ANTSPATH=/opt/ants' >> /etc/profile.d/nipype.sh && \
-    echo 'export PATH=$ANTSPATH:$PATH' >> /etc/profile.d/nipype.sh && \
-    echo 'source /etc/fsl/fsl.sh' >> /etc/profile.d/nipype.sh && \
-    echo 'source /etc/afni/afni.sh' >> /etc/profile.d/nipype.sh
+RUN echo '#!/bin/bash' > /etc/profile.d/nipype_deps.sh && \
+    echo 'export ANTSPATH=/opt/ants' >> /etc/profile.d/nipype_deps.sh && \
+    echo 'export PATH=$ANTSPATH:$PATH' >> /etc/profile.d/nipype_deps.sh && \
+    echo 'source /etc/fsl/fsl.sh' >> /etc/profile.d/nipype_deps.sh && \
+    echo 'source /etc/afni/afni.sh' >> /etc/profile.d/nipype_deps.sh
 
 # Clear apt cache to reduce image size
 RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
@@ -96,9 +96,9 @@ RUN echo "destinationFolder=/root/mcr" > mcr_options.txt && \
     unzip matlab_installer/installer.zip -d matlab_installer/ && \
     matlab_installer/install -inputFile mcr_options.txt && \
     rm -rf matlab_installer mcr_options.txt && \
-    echo 'export LD_LIBRARY_PATH=/root/mcr/v85/runtime/glnxa64:/root/mcr/v85/bin/glnxa64:/root/mcr/v85/sys/os/glnxa64:$LD_LIBRARY_PATH' >> /etc/profile.d/nipype.sh && \
-    echo 'export SPMMCRCMD="/root/spm12/run_spm12.sh /root/mcr/v85/ script"' >> /etc/profile.d/nipype.sh && \ 
-    echo 'export FORCE_SPMMCR=1' >> /etc/profile.d/nipype.sh
+    echo 'export LD_LIBRARY_PATH=/root/mcr/v85/runtime/glnxa64:/root/mcr/v85/bin/glnxa64:/root/mcr/v85/sys/os/glnxa64:$LD_LIBRARY_PATH' >> /etc/profile.d/nipype_deps.sh && \
+    echo 'export SPMMCRCMD="/root/spm12/run_spm12.sh /root/mcr/v85/ script"' >> /etc/profile.d/nipype_deps.sh && \ 
+    echo 'export FORCE_SPMMCR=1' >> /etc/profile.d/nipype_deps.sh
 
 ENV LD_LIBRARY_PATH "/root/mcr/v85/runtime/glnxa64:/root/mcr/v85/bin/glnxa64:/root/mcr/v85/sys/os/glnxa64:$LD_LIBRARY_PATH"
 ENV SPMMCRCMD "/root/spm12/run_spm12.sh /root/mcr/v85/ script"
@@ -109,7 +109,7 @@ RUN curl -sSL http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/sp
     unzip spm12.zip && \
     rm -rf spm12.zip
 
-RUN echo "source /etc/profile.d/nipype.sh" >> /etc/bash.bashrc
+RUN echo "source /etc/profile.d/nipype_deps.sh" >> /etc/bash.bashrc
 
 CMD ["/bin/bash"]
 

docker/test-image-nipype/Dockerfile

@@ -37,8 +37,8 @@ WORKDIR /root
 RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh && \
     /bin/bash Miniconda-latest-Linux-x86_64.sh -b -p /usr/local/miniconda && \
     rm Miniconda-latest-Linux-x86_64.sh && \
-    echo '#!/bin/bash' >> /etc/profile.d/anaconda.sh && \
-    echo 'export PATH=/usr/local/miniconda/bin:$PATH' >> /etc/profile.d/anaconda.sh
+    echo '#!/bin/bash' >> /etc/profile.d/nipype.sh && \
+    echo 'export PATH=/usr/local/miniconda/bin:$PATH' >> /etc/profile.d/nipype.sh
 
 ENV PATH /usr/local/miniconda/bin:$PATH
 
@@ -66,6 +66,5 @@ RUN conda create -y -n nipypetests-3.5 lockfile nipype python=3.5
 # RUN source activate nipypetests-2.7 && \
 #     pip install --upgrade pip && \
 
-
-
+RUN echo "source /etc/profile.d/nipype.sh" >> /etc/bash.bashrc
 CMD ["/bin/bash"]