Merge pull request #76 from fnothaft/bwakit

Use bwa-kit for alt aware alignment

bwa/Makefile

@@ -2,29 +2,31 @@
 build_output = runtime/bwa
 runtime_fullpath = $(realpath runtime)
 build_tool = runtime-container.DONE
+git_commit ?= $(shell git log --pretty=oneline -n 1 -- ../bwa | cut -f1 -d " ")
 name = quay.io/ucsc_cgl/bwa
-tag = 0.7.12
+tag = 0.7.12--${git_commit}
 
 # Steps
 build: ${build_output} ${build_tool}
 
 ${build_output}: build/Dockerfile
-	cd build && docker build -t ${name}-build:${tag} .
-	docker run -v ${runtime_fullpath}:/data ${name}-build:${tag} cp bwa /data
+	cd build && docker build -t bwabuild .
+	docker run -v ${runtime_fullpath}:/data bwabuild cp bwa /data
 
 ${build_tool}: ${build_output} runtime/Dockerfile
 	cd runtime && docker build -t ${name}:${tag} .
+	docker tag -f ${name}:${tag} ${name}:latest
+	docker rmi -f bwabuild
 	touch ${build_tool}
 
 push: build
 	# Requires ~/.dockercfg
 	docker push ${name}:${tag}
+	docker push ${name}:latest
 
 test: build
 	python test.py
 
 clean:
 	-rm ${build_tool}
 	-rm ${build_output}
-	docker rmi ${name}-build:${tag}
-	docker rmi ${name}:${tag}

bwa/build/Dockerfile

@@ -9,7 +9,4 @@ RUN git clone https://github.com/lh3/bwa.git
 
 WORKDIR /home/bwa
 
-# specifically check out 0.7.12 release tag
-RUN git checkout 0.7.12
-
 RUN make

bwakit/Dockerfile

@@ -0,0 +1,17 @@
+FROM ubuntu
+
+MAINTAINER Frank Austin Nothaft, fnothaft@berkeley.edu
+
+RUN apt-get update && \
+  apt-get install -y \
+    curl
+
+# pull down bwa-kit
+RUN curl -L http://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.12_x64-linux.tar.bz2 \
+  | tar -xjC /opt/
+
+# add wrapper script
+ADD wrapper.sh /opt/wrapper.sh
+
+# set entrypoint to bwakit
+ENTRYPOINT ["/opt/wrapper.sh"]

bwakit/Makefile

@@ -0,0 +1,19 @@
+build_tool = runtime-container.DONE
+nametag = quay.io/ucsc_cgl/bwakit:0.7.12
+
+build: ${build_tool}
+
+${build_tool}: Dockerfile
+	docker build -t ${nametag} .
+	touch ${build_tool}
+
+push: build
+	# Requires ~/.dockercfg 
+	docker push ${nametag}
+
+test: build
+	python test.py
+
+clean:
+	-rm ${build_tool}
+	docker rmi ${nametag}

bwa-postalt/test.py → bwakit/test.py

@@ -5,11 +5,11 @@
 import unittest
 
 
-class TestBWAPostalt(unittest.TestCase):
+class TestBWAKIT(unittest.TestCase):
 
     def test_docker_call(self):
-        out, err = check_docker_output(tool='quay.io/ucsc_cgl/bwa-postalt:0.7.12')
-        self.assertTrue('k8 bwa-postalt.js [options] <alt.sam> [aln.sam]' in out)
+        out, err = check_docker_output(tool='quay.io/ucsc_cgl/bwakit:0.7.12')
+        self.assertTrue('Map paired-end reads to GRCh38+ALT+decoy+HLA and perform HLA typing:' in out)
 
 def check_docker_output(tool):
     command = 'docker run ' + tool

bwakit/wrapper.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+/opt/bwa.kit/run-bwamem $@ | bash