Creating a Singularity recipe

Singularity

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+Bootstrap: shub
+#From: ubuntu:xenial
+From: vfonov/minc-toolkit-containers:1.9.16
+
+###################################################################
+#                                                                 #
+# MCIN (McGill Centre for Integrative Neuroscience)               #
+#                                                                 #
+# Singularity recipe for minc-bpipe-library to build a container  #
+# used in CBRAIN (https://github.com/aces/cbrain)                 #
+#                                                                 #
+###################################################################
+
+%labels
+  Maintainer Shawn Brown 
+
+%help
+This container provides minc-bpipe-library
+
+%post
+  apt-get update  -y
+  apt-get install -y automake
+  apt-get install -y build-essential 
+  apt-get install -y curl
+  apt-get install -y git
+  apt-get install -y libnetcdf-dev  
+  apt-get install -y libhdf5-dev
+  apt-get install -y parallel
+  apt-get install -y vim
+  apt-get install -y wget
+  apt-get install -y parallel
+  apt-get install -y default-jre
+  apt-get install -y default-jdk
+
+  curl "https://bootstrap.pypa.io/get-pip.py" -o "get-pip.py"
+  apt-get install -y python
+  python get-pip.py 
+  pip install pyminc scipy
+  pip install qbatch 
+  pip install future
+
+### Install Bpipe
+  export TERM=dumb
+  cd / 
+  #git clone https://github.com/ssadedin/bpipe.git
+  wget -P /tmp http://download.bpipe.org/versions/bpipe-0.9.9.6.tar.gz ; tar -xvzf /tmp/bpipe-0.9.9.6.tar.gz ; rm -rf /tmp/bpipe-0.9.9.6.tar.gz 
+  ln -sf /bpipe-0.9.9.6 /bpipe
+  cd /bpipe
+
+### get minc-to-bpipe 
+  cd /
+  git clone https://github.com/CobraLab/minc-bpipe-library.git
+  rm -rf /minc-bpipe-library/bpipe.config
+
+%environment
+  PATH=/bpipe/bin:$PATH
+
+%runscript
+