Merge pull request #163 from satra/enh/antsupdate

Enh/antsupdate

Author: binarybottle

install/Dockerfile

@@ -1,5 +1,5 @@
-# Generated by Neurodocker version 0.4.1
-# Timestamp: 2018-10-05 14:45:31 UTC
+# Generated by Neurodocker version 0.4.2
+# Timestamp: 2018-11-06 01:58:12 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -135,7 +135,7 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
            nose \
     && sync && conda clean -tipsy && sync \
     && bash -c "source activate mb \
-    &&   pip install  --no-cache-dir \
+    &&   pip install --no-cache-dir  \
              datalad[full] \
              duecredit" \
     && rm -rf ~/.cache/pip/* \
@@ -148,13 +148,19 @@ RUN mkdir -p /opt/data && cd /opt/data && \
            curl -sSL https://osf.io/download/rh9km/?revision=2 -o templates.zip && \
            unzip templates.zip && \
            rm -f /opt/data/templates.zip && \
+           curl -sSL https://files.osf.io/v1/resources/hvc52/providers/osfstorage/57c1a8f06c613b01f98d68a9/?zip= -o OASIS-TRT-20_brains.zip && \
+           mkdir OASIS-TRT-20_brains && \
+           cd OASIS-TRT-20_brains && \
+           unzip ../OASIS-TRT-20_brains.zip && \
+           cd .. && \
+           rm OASIS-TRT-20_brains.zip && \
+           curl -sSL https://files.osf.io/v1/resources/zevma/providers/osfstorage/5783dfcab83f6901f963735c/?zip= -o cmalabels.zip && \
+           mkdir OASIS-TRT-20_DKT31_CMA_labels_v2 && \
+           cd OASIS-TRT-20_DKT31_CMA_labels_v2 && \
+           unzip ../cmalabels.zip && \
+           cd .. && \
+           rm cmalabels.zip && \
            curl -sSL https://osf.io/download/d2cmy/ -o OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_OASIS-30_v2.nii.gz && \
-           curl -sSL https://osf.io/download/qz3kx/ -o OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
-           tar zxf OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
-           rm OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
-           curl -sSL https://osf.io/download/dcf94/ -o OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
-           tar zxf OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
-           rm OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
            rm -rf __MACOSX
 
 RUN bash -c 'source /opt/miniconda-latest/etc/profile.d/conda.sh && \
@@ -262,7 +268,7 @@ RUN echo '{ \
     \n    ], \
     \n    [ \
     \n      "run", \
-    \n      "mkdir -p /opt/data && cd /opt/data && \\\\n    curl -sSL https://osf.io/download/rh9km/?revision=2 -o templates.zip && \\\\n    unzip templates.zip && \\\\n    rm -f /opt/data/templates.zip && \\\\n    curl -sSL https://osf.io/download/d2cmy/ -o OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_OASIS-30_v2.nii.gz && \\\\n    curl -sSL https://osf.io/download/qz3kx/ -o OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \\\\n    tar zxf OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \\\\n    rm OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \\\\n    curl -sSL https://osf.io/download/dcf94/ -o OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \\\\n    tar zxf OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \\\\n    rm OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \\\\n    rm -rf __MACOSX" \
+    \n      "mkdir -p /opt/data && cd /opt/data && \\\\n    curl -sSL https://osf.io/download/rh9km/?revision=2 -o templates.zip && \\\\n    unzip templates.zip && \\\\n    rm -f /opt/data/templates.zip && \\\\n    curl -sSL https://files.osf.io/v1/resources/hvc52/providers/osfstorage/57c1a8f06c613b01f98d68a9/?zip= -o OASIS-TRT-20_brains.zip && \\\\n    mkdir OASIS-TRT-20_brains && \\\\n    cd OASIS-TRT-20_brains && \\\\n    unzip ../OASIS-TRT-20_brains.zip && \\\\n    cd .. && \\\\n    rm OASIS-TRT-20_brains.zip && \\\\n    curl -sSL https://files.osf.io/v1/resources/zevma/providers/osfstorage/5783dfcab83f6901f963735c/?zip= -o cmalabels.zip && \\\\n    mkdir OASIS-TRT-20_DKT31_CMA_labels_v2 && \\\\n    cd OASIS-TRT-20_DKT31_CMA_labels_v2 && \\\\n    unzip ../cmalabels.zip && \\\\n    cd .. && \\\\n    rm cmalabels.zip && \\\\n    curl -sSL https://osf.io/download/d2cmy/ -o OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_OASIS-30_v2.nii.gz && \\\\n    rm -rf __MACOSX" \
     \n    ], \
     \n    [ \
     \n      "run_bash", \

install/neurodocker.sh

@@ -44,7 +44,7 @@
 ###############################################################################
 
 # Generate a dockerfile for building a mindboggle container
-docker run --rm kaczmarj/neurodocker:0.4.1 generate docker \
+docker run --rm kaczmarj/neurodocker:0.4.2 generate docker \
   --base neurodebian:stretch \
   --pkg-manager apt \
   --install graphviz tree git-annex-standalone vim \
@@ -64,13 +64,19 @@ docker run --rm kaczmarj/neurodocker:0.4.1 generate docker \
     curl -sSL https://osf.io/download/rh9km/?revision=2 -o templates.zip && \
     unzip templates.zip && \
     rm -f /opt/data/templates.zip && \
+    curl -sSL https://files.osf.io/v1/resources/hvc52/providers/osfstorage/57c1a8f06c613b01f98d68a9/?zip= -o OASIS-TRT-20_brains.zip && \
+    mkdir OASIS-TRT-20_brains && \
+    cd OASIS-TRT-20_brains && \
+    unzip ../OASIS-TRT-20_brains.zip && \
+    cd .. && \
+    rm OASIS-TRT-20_brains.zip && \
+    curl -sSL https://files.osf.io/v1/resources/zevma/providers/osfstorage/5783dfcab83f6901f963735c/?zip= -o cmalabels.zip && \
+    mkdir OASIS-TRT-20_DKT31_CMA_labels_v2 && \
+    cd OASIS-TRT-20_DKT31_CMA_labels_v2 && \
+    unzip ../cmalabels.zip && \
+    cd .. && \
+    rm cmalabels.zip && \
     curl -sSL https://osf.io/download/d2cmy/ -o OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_OASIS-30_v2.nii.gz && \
-    curl -sSL https://osf.io/download/qz3kx/ -o OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
-    tar zxf OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
-    rm OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
-    curl -sSL https://osf.io/download/dcf94/ -o OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
-    tar zxf OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
-    rm OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
     rm -rf __MACOSX' \
   --run-bash 'source /opt/miniconda-latest/etc/profile.d/conda.sh && \
         conda activate mb && \

mindboggle/mindboggle

@@ -182,6 +182,8 @@ adv_args.add_argument("--plugin", dest="plugin",
                       help="nipype plugin (see nipype documentation)")
 adv_args.add_argument("--plugin_args", dest="plugin_args",
                       help="plugin arguments (see nipype documentation)")
+adv_args.add_argument("--prov", action='store_true',
+                      help="Capture provenance")
 args = parser.parse_args()
 
 # ----------------------------------------------------------------------------
@@ -2361,7 +2363,8 @@ if __name__ == '__main__':
     # ------------------------------------------------------------------------
     # Workflow configuration: provenance tracking, content hashing, etc.:
     # ------------------------------------------------------------------------
-    # config.enable_provenance()
+    if args.prov:
+        config.enable_provenance()
     mbFlow.config['execution']['hash_method'] = 'content'
     # mbFlow.config['execution']['use_relative_paths'] = True