From 01e50faf87df96ad3d74fa5bd0b33f7d18bfcfb3 Mon Sep 17 00:00:00 2001
From: akhanf <alik@robarts.ca>
Date: Sun, 14 Jan 2018 20:27:43 -0500
Subject: [PATCH] added releases for shub

---
 Singularity.v0.0.1 | 55 ++++++++++++++++++++++++++++++++++++++++++++++
 Singularity.v0.0.2 | 55 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 110 insertions(+)
 create mode 100644 Singularity.v0.0.1
 create mode 100644 Singularity.v0.0.2

diff --git a/Singularity.v0.0.1 b/Singularity.v0.0.1
new file mode 100644
index 0000000..8e12b6d
--- /dev/null
+++ b/Singularity.v0.0.1
@@ -0,0 +1,55 @@
+Bootstrap: shub
+From: khanlab/neuroglia-dwi
+
+%labels
+Maintainer "Ali Khan"
+
+#########
+%setup
+#########
+mkdir -p $SINGULARITY_ROOTFS/opt/vasst-dev
+cp -Rv . $SINGULARITY_ROOTFS/opt/vasst-dev
+
+#########
+%post
+#########
+
+SINGULARITY_TAG=${SINGULARITY_BUILDDEF#Singularity.}
+
+cd /opt/vasst-dev
+if [ ! "$SINGULARITY_TAG" = "Singularity" ]
+then
+  git checkout $SINGULARITY_TAG
+fi
+
+echo addpath\(genpath\(\'${PIPELINE_TOOL_DIR}/matlab\'\)\)\; >> /etc/octave.conf 
+
+cd /opt/vasst-dev/install_scripts
+export DEBIAN_FRONTEND=noninteractive
+
+bash 05.install_MCR.sh /opt v92 R2017a
+bash 27.install_vasst_dev_atlases_by_source.sh /opt
+
+
+#########
+%environment
+
+
+
+#vasst-dev
+export VASST_DEV_HOME=/opt/vasst-dev
+export PIPELINE_ATLAS_DIR=/opt/atlases
+export PIPELINE_DIR=$VASST_DEV_HOME/pipeline
+export PIPELINE_TOOL_DIR=$VASST_DEV_HOME/tools
+MIAL_DEPENDS_DIR=$VASST_DEV_HOME/mial-depends
+#MIAL_DEPENDS_LIBS=$VASST_DEV_HOME/mial-depends/lib
+#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MIAL_DEPENDS_LIBS
+export PIPELINE_CFG_DIR=$PIPELINE_DIR/cfg
+export PATH=$PIPELINE_TOOL_DIR:$MIAL_DEPENDS_DIR:$PATH
+export MCRBINS=$VASST_DEV_HOME/mcr/v92
+for name in `ls -d $PIPELINE_DIR/*`; do  export PATH=$name:$PATH; done
+#mcr - vasst-dev dependency
+export MCRROOT=/opt/mcr/v92
+
+
+
diff --git a/Singularity.v0.0.2 b/Singularity.v0.0.2
new file mode 100644
index 0000000..8e12b6d
--- /dev/null
+++ b/Singularity.v0.0.2
@@ -0,0 +1,55 @@
+Bootstrap: shub
+From: khanlab/neuroglia-dwi
+
+%labels
+Maintainer "Ali Khan"
+
+#########
+%setup
+#########
+mkdir -p $SINGULARITY_ROOTFS/opt/vasst-dev
+cp -Rv . $SINGULARITY_ROOTFS/opt/vasst-dev
+
+#########
+%post
+#########
+
+SINGULARITY_TAG=${SINGULARITY_BUILDDEF#Singularity.}
+
+cd /opt/vasst-dev
+if [ ! "$SINGULARITY_TAG" = "Singularity" ]
+then
+  git checkout $SINGULARITY_TAG
+fi
+
+echo addpath\(genpath\(\'${PIPELINE_TOOL_DIR}/matlab\'\)\)\; >> /etc/octave.conf 
+
+cd /opt/vasst-dev/install_scripts
+export DEBIAN_FRONTEND=noninteractive
+
+bash 05.install_MCR.sh /opt v92 R2017a
+bash 27.install_vasst_dev_atlases_by_source.sh /opt
+
+
+#########
+%environment
+
+
+
+#vasst-dev
+export VASST_DEV_HOME=/opt/vasst-dev
+export PIPELINE_ATLAS_DIR=/opt/atlases
+export PIPELINE_DIR=$VASST_DEV_HOME/pipeline
+export PIPELINE_TOOL_DIR=$VASST_DEV_HOME/tools
+MIAL_DEPENDS_DIR=$VASST_DEV_HOME/mial-depends
+#MIAL_DEPENDS_LIBS=$VASST_DEV_HOME/mial-depends/lib
+#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MIAL_DEPENDS_LIBS
+export PIPELINE_CFG_DIR=$PIPELINE_DIR/cfg
+export PATH=$PIPELINE_TOOL_DIR:$MIAL_DEPENDS_DIR:$PATH
+export MCRBINS=$VASST_DEV_HOME/mcr/v92
+for name in `ls -d $PIPELINE_DIR/*`; do  export PATH=$name:$PATH; done
+#mcr - vasst-dev dependency
+export MCRROOT=/opt/mcr/v92
+
+
+