Update to latest (1.0dev100) release of snap (resolves BD2KGenomics#261)

snap/Dockerfile

@@ -1,13 +1,15 @@
-FROM ubuntu:14.04
+FROM ubuntu
 
-RUN apt-get update && \
-  apt-get install -y python libnss3 wget
+RUN apt-get update && apt-get install -y git build-essential zlib1g-dev
 
-# Download SNAP binary
-RUN mkdir /opt/SNAP
-WORKDIR /opt/SNAP
-RUN wget http://snap.cs.berkeley.edu/downloads/snap-beta.18-linux.tar.gz
-RUN tar xzvf snap-beta.18-linux.tar.gz
-RUN chmod +x snap-aligner
+# clone snap
+WORKDIR /opt/
+RUN git clone https://github.com/amplab/snap.git
+WORKDIR /opt/snap
+RUN git checkout 48e7ae5d38145c094af1fe42a4b3abf1e72e1bb7
 
-ENTRYPOINT ["/opt/SNAP/snap-aligner"]
+# build snap
+WORKDIR /opt/snap/
+RUN make
+
+ENTRYPOINT ["/opt/snap/snap-aligner"]

snap/Makefile

@@ -1,11 +1,12 @@
 build_tool = runtime-container.DONE
-git_commit ?= $(shell git log --pretty=oneline -n 1 -- ../snap| cut -f1 -d " ")
+git_commit ?= $(shell git log --pretty=oneline -n 1 -- ../snap ../cmake | cut -f1 -d " ")
 name = quay.io/ucsc_cgl/snap
-tag = 1.0beta.18--${git_commit}
+tag = 1.0dev.100--${git_commit}
 
 build: ${build_tool}
 
 ${build_tool}: Dockerfile
+	cd ../cmake && $(MAKE) build
 	docker build -t ${name}:${tag} .
 	docker tag -f ${name}:${tag} ${name}:latest
 	touch ${build_tool}

snap/test.py

@@ -9,7 +9,7 @@ class TestSNAP(unittest.TestCase):
 
     def test_docker_call(self):
         out, err = check_docker_output('quay.io/ucsc_cgl/snap:latest')
-        self.assertTrue('Welcome to SNAP version 1.0beta.18.' in out)
+        self.assertTrue('Welcome to SNAP version 1.0dev.100.' in out)
 
 def check_docker_output(cmd):
     command = 'docker run ' + cmd