FIX: use more recent heudiconv

Author: mvdoc

Dockerfile

@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.4.0.dev2
-# Timestamp: 2018-05-12 17:03:02 UTC
+# Timestamp: 2018-05-22 19:25:04 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -76,7 +76,7 @@ RUN npm install -g [email protected]
 
 RUN mkdir /afs /inbox
 
-RUN pip install heudiconv[all]
+RUN pip install git+https://github.com/nipy/heudiconv.git@d3b7077bd24afcae459531889263dde08ae50466
 
 ENV PATH="/opt/dcm2niix-v1.0.20180328/bin:$PATH"
 RUN apt-get update -qq \
@@ -101,7 +101,7 @@ RUN apt-get update -qq \
     && make install \
     && rm -rf /tmp/dcm2niix
 
-RUN echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'if [ -z "$@" ]; then heudiconv -h; else heudiconv "$@"; fi' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh
+RUN echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'heudiconv "$@"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh
 
 RUN useradd --no-user-group --create-home --shell /bin/bash reproin
 USER reproin
@@ -160,7 +160,7 @@ RUN echo '{ \
     \n    ], \
     \n    [ \
     \n      "run", \
-    \n      "pip install heudiconv[all]" \
+    \n      "pip install git+https://github.com/nipy/heudiconv.git@d3b7077bd24afcae459531889263dde08ae50466" \
     \n    ], \
     \n    [ \
     \n      "dcm2niix", \
@@ -171,7 +171,7 @@ RUN echo '{ \
     \n    ], \
     \n    [ \
     \n      "run", \
-    \n      "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'if [ -z \"$@\" ]; then heudiconv -h; else heudiconv \"$@\"; fi'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh" \
+    \n      "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'heudiconv \"$@\"'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh" \
     \n    ], \
     \n    [ \
     \n      "user", \

Singularity

@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.4.0.dev2
-# Timestamp: 2018-05-12 17:03:04 UTC
+# Timestamp: 2018-05-22 19:25:06 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -71,7 +71,7 @@ npm install -g [email protected]
 
 mkdir /afs /inbox
 
-pip install heudiconv[all]
+pip install git+https://github.com/nipy/heudiconv.git@d3b7077bd24afcae459531889263dde08ae50466
 
 apt-get update -qq
 apt-get install -y -q --no-install-recommends \
@@ -95,7 +95,7 @@ make
 make install
 rm -rf /tmp/dcm2niix
 
-echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'if [ -z "$@" ]; then heudiconv -h; else heudiconv "$@"; fi' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh
+echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'heudiconv "$@"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh
 
 useradd --no-user-group --create-home --shell /bin/bash reproin
 su - reproin
@@ -159,7 +159,7 @@ echo '{
 \n    ],
 \n    [
 \n      "run",
-\n      "pip install heudiconv[all]"
+\n      "pip install git+https://github.com/nipy/heudiconv.git@d3b7077bd24afcae459531889263dde08ae50466"
 \n    ],
 \n    [
 \n      "dcm2niix",
@@ -170,7 +170,7 @@ echo '{
 \n    ],
 \n    [
 \n      "run",
-\n      "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'if [ -z \"$@\" ]; then heudiconv -h; else heudiconv \"$@\"; fi'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh"
+\n      "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'heudiconv \"$@\"'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh"
 \n    ],
 \n    [
 \n      "user",

generate_container.sh

@@ -12,9 +12,9 @@ generate() {
     --install nodejs npm \
     --run "npm install -g [email protected]" \
     --run "mkdir /afs /inbox" \
-    --run "pip install heudiconv[all]" \
+    --run "pip install git+https://github.com/nipy/heudiconv.git@d3b7077bd24afcae459531889263dde08ae50466" \
     --dcm2niix version="v1.0.20180328" method="source" \
-    --run "echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'if [ -z \"\$@\" ]; then heudiconv -h; else heudiconv \"\$@\"; fi' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh" \
+    --run "echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'heudiconv \"\$@\"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh" \
     --user=reproin \
     --entrypoint "/neurodocker/heudiconv.sh"
 }