From 629e60a02531f022996b3704d4bed29850f9e86b Mon Sep 17 00:00:00 2001
From: tobiasrausch <rauschtobi@gmail.com>
Date: Thu, 11 Jul 2019 09:44:27 +0200
Subject: [PATCH] added tracy singularity definition file

---
 singularity/README.md |  7 +++++++
 singularity/tracy.def | 44 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+)
 create mode 100644 singularity/README.md
 create mode 100644 singularity/tracy.def

diff --git a/singularity/README.md b/singularity/README.md
new file mode 100644
index 0000000..dfdc249
--- /dev/null
+++ b/singularity/README.md
@@ -0,0 +1,7 @@
+You can build a [tracy](https://github.com/gear-genomics/tracy) singularity container (SIF file) using
+
+`sudo singularity build tracy.sif tracy.def`
+
+Once you have built the container you can run analysis using
+
+`singularity exec tracy.sif tracy basecall input.ab1`
diff --git a/singularity/tracy.def b/singularity/tracy.def
new file mode 100644
index 0000000..05570c8
--- /dev/null
+++ b/singularity/tracy.def
@@ -0,0 +1,44 @@
+# Build image
+BootStrap: library
+From: ubuntu:16.04
+Stage: build
+
+%post
+	apt-get -y update
+	apt-get install -y build-essential cmake g++ gfortran git hdf5-tools libboost-date-time-dev libboost-program-options-dev libboost-system-dev libboost-filesystem-dev libboost-iostreams-dev libbz2-dev libhdf5-dev libncurses-dev liblzma-dev zlib1g-dev
+	apt-get clean
+	rm -rf /var/lib/apt/lists/*
+	cd /opt
+	git clone --recursive https://github.com/gear-genomics/tracy.git
+	cd /opt/tracy/
+	make STATIC=1 all
+	make install
+
+
+# Final image
+BootStrap: library
+From: alpine:3.9
+Stage: final
+
+%files from build
+       /opt/tracy/bin/tracy /bin/tracy
+
+%post
+	TRACYVERSION=`./bin/tracy --version`
+	echo "export TRACYVERSION=\"${TRACYVERSION}\"" >> $SINGULARITY_ENVIRONMENT
+	CREATEDATE=`date`
+	echo "export CREATEDATE=\"${CREATEDATE}\"" >> $SINGULARITY_ENVIRONMENT
+
+%environment
+	export PATH=/bin:$PATH
+
+%runscript
+	tracy
+
+%labels
+	Singularity definition file version v0.0.1
+
+%help
+	This is a container running tracy.
+	You can run tracy on files inside the directory where you start
+	the container, i.e.: singularity exec tracy.sif tracy basecall input.ab1