[DATALAD RUNCMD] ./generate_container.sh

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "./generate_container.sh",
 "exit": 0,
 "inputs": [],
 "outputs": [
  "Singularity",
  "Dockerfile"
 ],
 "pwd": "."
}
^^^ Do not change lines above ^^^

Author: yarikoptic

Dockerfile

@@ -1,5 +1,5 @@
-# Generated by Neurodocker version 0.4.1-dev
-# Timestamp: 2018-07-22 14:48:52 UTC
+# Generated by Neurodocker version 0.4.1
+# Timestamp: 2019-01-05 04:54:54 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -50,6 +50,7 @@ RUN apt-get update -qq \
            curl \
            procps \
            datalad \
+           pigz \
            git-annex-standalone \
            python-nipype \
            virtualenv \
@@ -74,13 +75,13 @@ RUN apt-get update -qq \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-RUN npm install -g bids-validator@0.26.11
+RUN npm install -g bids-validator@1.1.1
 
 RUN mkdir /afs /inbox
 
 RUN pip install heudiconv
 
-ENV PATH="/opt/dcm2niix-v1.0.20180622/bin:$PATH"
+ENV PATH="/opt/dcm2niix-v1.0.20181125/bin:$PATH"
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
            cmake \
@@ -95,10 +96,10 @@ RUN apt-get update -qq \
     && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
     && cd /tmp/dcm2niix \
     && git fetch --tags \
-    && git checkout v1.0.20180622 \
+    && git checkout v1.0.20181125 \
     && mkdir /tmp/dcm2niix/build \
     && cd /tmp/dcm2niix/build \
-    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20180622 .. \
+    && cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20181125 .. \
     && make \
     && make install \
     && rm -rf /tmp/dcm2niix
@@ -129,6 +130,7 @@ RUN echo '{ \
     \n        "curl", \
     \n        "procps", \
     \n        "datalad", \
+    \n        "pigz", \
     \n        "git-annex-standalone", \
     \n        "python-nipype", \
     \n        "virtualenv", \
@@ -156,7 +158,7 @@ RUN echo '{ \
     \n    ], \
     \n    [ \
     \n      "run", \
-    \n      "npm install -g bids-validator@0.26.11" \
+    \n      "npm install -g bids-validator@1.1.1" \
     \n    ], \
     \n    [ \
     \n      "run", \
@@ -169,7 +171,7 @@ RUN echo '{ \
     \n    [ \
     \n      "dcm2niix", \
     \n      { \
-    \n        "version": "v1.0.20180622", \
+    \n        "version": "v1.0.20181125", \
     \n        "method": "source" \
     \n      } \
     \n    ], \

Singularity

@@ -1,5 +1,5 @@
-# Generated by Neurodocker version 0.4.1-dev
-# Timestamp: 2018-07-22 14:48:54 UTC
+# Generated by Neurodocker version 0.4.1
+# Timestamp: 2019-01-05 04:54:55 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -45,6 +45,7 @@ apt-get install -y -q --no-install-recommends \
     curl \
     procps \
     datalad \
+    pigz \
     git-annex-standalone \
     python-nipype \
     virtualenv \
@@ -69,7 +70,7 @@ apt-get install -y -q --no-install-recommends \
 apt-get clean
 rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-npm install -g bids-validator@0.26.11
+npm install -g bids-validator@1.1.1
 
 mkdir /afs /inbox
 
@@ -89,10 +90,10 @@ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix
 cd /tmp/dcm2niix
 git fetch --tags
-git checkout v1.0.20180622
+git checkout v1.0.20181125
 mkdir /tmp/dcm2niix/build
 cd /tmp/dcm2niix/build
-cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20180622 ..
+cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20181125 ..
 make 
 make install
 rm -rf /tmp/dcm2niix
@@ -128,6 +129,7 @@ echo '{
 \n        "curl",
 \n        "procps",
 \n        "datalad",
+\n        "pigz",
 \n        "git-annex-standalone",
 \n        "python-nipype",
 \n        "virtualenv",
@@ -155,7 +157,7 @@ echo '{
 \n    ],
 \n    [
 \n      "run",
-\n      "npm install -g bids-validator@0.26.11"
+\n      "npm install -g bids-validator@1.1.1"
 \n    ],
 \n    [
 \n      "run",
@@ -168,7 +170,7 @@ echo '{
 \n    [
 \n      "dcm2niix",
 \n      {
-\n        "version": "v1.0.20180622",
+\n        "version": "v1.0.20181125",
 \n        "method": "source"
 \n      }
 \n    ],
@@ -191,7 +193,7 @@ echo '{
 export LANG="en_US.UTF-8"
 export LC_ALL="en_US.UTF-8"
 export ND_ENTRYPOINT="/neurodocker/startup.sh"
-export PATH="/opt/dcm2niix-v1.0.20180622/bin:$PATH"
+export PATH="/opt/dcm2niix-v1.0.20181125/bin:$PATH"
 
 %runscript
 /neurodocker/heudiconv.sh