Merge pull request #164 from mgxd/enh/antsupdate

enh: play nice with provenance

Author: satra

install/Dockerfile

@@ -1,5 +1,5 @@
-# Generated by Neurodocker version 0.4.2
-# Timestamp: 2018-11-06 01:58:12 UTC
+# Generated by Neurodocker version 0.4.2-3-gf7055a1
+# Timestamp: 2018-11-26 23:42:54 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -121,23 +121,23 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
     && sync && conda clean -tipsy && sync \
     && conda create -y -q --name mb \
     && conda install -y -q --name mb \
-           python=3.6 \
-           pip \
-           jupyter \
-           cmake \
-           mesalib \
-           vtk \
-           pandas \
-           matplotlib \
-           colormath \
-           nipype \
-           tbb-devel \
-           nose \
+           'python=3.6' \
+           'pip' \
+           'jupyter' \
+           'cmake' \
+           'mesalib' \
+           'vtk' \
+           'pandas' \
+           'matplotlib' \
+           'colormath' \
+           'nipype>=1.1.4' \
+           'tbb-devel' \
+           'nose' \
     && sync && conda clean -tipsy && sync \
     && bash -c "source activate mb \
     &&   pip install --no-cache-dir  \
-             datalad[full] \
-             duecredit" \
+             'datalad[full]' \
+             'duecredit'" \
     && rm -rf ~/.cache/pip/* \
     && sync \
     && sed -i '$isource activate mb' $ND_ENTRYPOINT
@@ -250,7 +250,7 @@ RUN echo '{ \
     \n          "pandas", \
     \n          "matplotlib", \
     \n          "colormath", \
-    \n          "nipype", \
+    \n          "nipype>=1.1.4", \
     \n          "tbb-devel", \
     \n          "nose" \
     \n        ], \

install/neurodocker.sh

@@ -43,8 +43,10 @@
 # docker run --rm -ti -v $HOST:/home/jovyan/work nipy/mindboggle $IMAGE --id $ID --out $OUT
 ###############################################################################
 
+image="kaczmarj/neurodocker:master@sha256:936401fe8f677e0d294f688f352cbb643c9693f8de371475de1d593650e42a66"
+
 # Generate a dockerfile for building a mindboggle container
-docker run --rm kaczmarj/neurodocker:0.4.2 generate docker \
+docker run --rm ${image} generate docker \
   --base neurodebian:stretch \
   --pkg-manager apt \
   --install graphviz tree git-annex-standalone vim \
@@ -54,8 +56,8 @@ docker run --rm kaczmarj/neurodocker:0.4.2 generate docker \
   --ants version=b43df4bfc8 method=source cmake_opts='-DBUILD_SHARED_LIBS=ON' make_opts='-j 4'\
   --run 'ln -s /usr/lib/x86_64-linux-gnu /usr/lib64' \
   --miniconda \
-    conda_install="python=3.6 pip jupyter cmake mesalib vtk pandas \
-      matplotlib colormath nipype tbb-devel nose" \
+    conda_install="python=3.6 pip jupyter cmake mesalib vtk pandas
+      matplotlib colormath nipype>=1.1.4 tbb-devel nose" \
     pip_install="datalad[full] duecredit" \
     create_env="mb" \
     activate=true \

mindboggle/mindboggle

@@ -348,6 +348,10 @@ def first_string_containing_substring(substring, List):
     first_matching_string = [x for x in List if substring in x][0]
     return first_matching_string
 
+# Ensure provenance configuration is inherited by workflow
+if args.prov:
+    config.enable_provenance()
+
 # ============================================================================
 #
 #   Initialize workflow inputs and outputs
@@ -2361,11 +2365,10 @@ if __name__ == '__main__':
     time0 = time()
 
     # ------------------------------------------------------------------------
-    # Workflow configuration: provenance tracking, content hashing, etc.:
+    # Workflow configuration: content hashing, crashfiles, etc.:
     # ------------------------------------------------------------------------
-    if args.prov:
-        config.enable_provenance()
     mbFlow.config['execution']['hash_method'] = 'content'
+    mbFlow.config['execution']['crashfile_format'] = 'txt'
     # mbFlow.config['execution']['use_relative_paths'] = True
 
     # ------------------------------------------------------------------------

mindboggle/mindboggle123

@@ -130,6 +130,10 @@ TDIR = args.template
 if args.skip_freesurfer and args.skip_ants:
     print("Use only one of the skip arguments: --skip_freesurfer, --skip_ants.")
 
+# Ensure provenance configuration is inherited by workflow
+if args.prov:
+    config.enable_provenance()
+
 # ----------------------------------------------------------------------------
 # Initialize workflow inputs and outputs
 # ----------------------------------------------------------------------------
@@ -445,10 +449,8 @@ if __name__ == '__main__':
     time0 = time()
 
     # --------------------------------------------------------------------
-    # Workflow configuration: provenance tracking, content hashing, etc.:
+    # Workflow configuration: content hashing, crashfiles, etc.:
     # --------------------------------------------------------------------
-    if args.prov:
-        config.enable_provenance()
     mbFlow.config['execution']['hash_method'] = 'content'
     # mbFlow.config['execution']['use_relative_paths'] = True
     mbFlow.config['execution']['crashfile_format'] = 'txt'