Merge pull request #32 from FredHutch/master

Add Dockerfile and wrapper script

Dockerfile

@@ -0,0 +1,26 @@
+FROM ubuntu:16.04
+MAINTAINER sminot@fredhutch.org
+
+# Install prerequisites
+RUN apt update && \
+	apt-get install -y libcurl4-openssl-dev git make gcc \
+					   zlib1g-dev wget unzip python2.7 \
+					   python-dev python-pip bats awscli curl && \
+	pip install boto3==1.4.7
+
+# Set the default langage to C
+ENV LC_ALL C
+
+# Import the repo to /usr/bin/paladin
+RUN mkdir /usr/bin/paladin
+ADD . /usr/bin/paladin/
+RUN cd /usr/bin/paladin && \
+    make && \
+    ln -s /usr/bin/paladin/paladin /usr/local/bin/ && \
+    ln -s /usr/bin/paladin/run.py /usr/local/bin/
+
+# Test the installation
+RUN cd /usr/bin/paladin/sample_data && \
+	bash make_test.sh && \
+	cd /usr/bin/paladin && \
+	rm -r sample_data

README.md

@@ -25,6 +25,12 @@ make
 PATH=$PATH:$(pwd)
 ```
 
+**Docker**
+
+Alternatively, you can use Paladin with the Docker image hosted at [https://quay.io/repository/fhcrc-microbiome/paladin](https://quay.io/repository/fhcrc-microbiome/paladin). This image can be downloaded with the command `docker pull quay.io/fhcrc-microbiome/paladin`. A set of tags are used to pin releases, e.g. `v1.4.0--1` is the image pinned to the `v1.4.0` version of Paladin. 
+
+[![Docker Repository on Quay](https://quay.io/repository/fhcrc-microbiome/paladin/status "Docker Repository on Quay")](https://quay.io/repository/fhcrc-microbiome/paladin)
+
 SAMPLE COMMANDS
 --
 
@@ -70,6 +76,10 @@ paladin align -t 4 -o lungstudy uniprot_sprot.fasta.gz SRR1177122.fastq.gz
 #look at report file, SAM, etc.
 ```
 
+**Wrapper script**
+
+This repo also contains a wrapper script (`run.py`) which is intended to make it easier to deploy Paladin on cloud or HPC computing resources (e.g. Slurm or AWS). The script is located in the PATH in the Docker image, and so you can run `run.py -h` to see the set of options for this script. In brief, users can specify the input URL, reference database path, and output folder location (any of which may be local paths, S3 buckets, or FTP). The run script will fetch the input data, run Paladin, wrap up the results into a single JSON output file, and copy the results to the specified output folder. 
+
 OUTPUT
 --