Merge branch 'master' into develop

In preparation for 2.0.0 release.

Dockerfile

@@ -1,21 +1,20 @@
 FROM ubuntu:latest
 MAINTAINER Shaun Jackman <sjackman@gmail.com>
 
-ADD . /root/abyss
-RUN apt-get update && \
-	apt-get install -y \
-		automake \
-		g++ \
-		libboost-dev \
-		libopenmpi-dev \
-		libsparsehash-dev \
-		libsqlite3-dev \
-		make
-RUN cd /root/abyss \
+RUN apt-get update \
+	&& apt-get install -y --no-install-recommends \
+		make openmpi-bin ssh
+ADD . /tmp/abyss
+RUN apt-get install -y --no-install-recommends \
+		automake g++ libboost-dev libopenmpi-dev libsparsehash-dev \
+	&& cd /tmp/abyss \
 	&& ./autogen.sh \
 	&& mkdir build && cd build \
 	&& ../configure --with-mpi=/usr/lib/openmpi \
 	&& make install-strip \
-	&& rm -rf /root/abyss
+	&& rm -rf /tmp/abyss \
+	&& apt-get autoremove -y binutils \
+		automake g++ libboost-dev libopenmpi-dev libsparsehash-dev
+ENV SHELL=/bin/bash
 ENTRYPOINT ["abyss-pe"]
 CMD ["help"]

bin/abyss-dida

@@ -71,7 +71,7 @@ fi
 # Add file arguments to dida command.  Convert all input file paths
 # to absolute, since we change to a temp dir below
 
-query=($(readlink -f "$@"))
+query=($(echo "$@" | xargs -n1 readlink -f))
 target=${query[${#query[@]}-1]}
 unset query[${#query[@]}-1]