Merge branch 'release/1.25'

Author: briandoconnor

Dockerfile

@@ -10,9 +10,13 @@ MAINTAINER Brian O'Connor <briandoconnor@gmail.com>
 
 # Setup packages
 USER root
-RUN apt-get -m update && apt-get install -y apt-utils tar git curl nano wget dialog net-tools build-essential time
+RUN apt-get -m update && apt-get install -y wget unzip openjdk-7-jre zip
 
 # get the tool
 RUN wget -q http://downloads.sourceforge.net/project/bamstats/BAMStats-1.25.zip
-RUN unzip BAMStats-1.25.zip
+RUN unzip BAMStats-1.25.zip && \
+    rm BAMStats-1.25.zip && \
+    mv BAMStats-1.25 /opt/
+COPY bin/bamstats /usr/local/bin/
+RUN chmod a+x /usr/local/bin/bamstats
 CMD ["/bin/bash"]

Dockstore.cwl

@@ -0,0 +1,39 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+description: "A Docker container for the BAMStats command. See the [BAMStats](http://bamstats.sourceforge.net/) website for more information."
+id: "BAMStats"
+label: "BAMStats tool"
+
+dct:creator:
+  "@id": "http://orcid.org/0000-0002-7681-6415"
+  foaf:name: Brian O'Connor
+  foaf:mbox: "mailto:briandoconnor@gmail.com"
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: "quay.io/briandoconnor/dockstore-tool-bamstats:1.25"
+  - { import: node-engine.cwl }
+
+hints:
+  - class: ResourceRequirement
+    coresMin: 1
+    ramMin: 4092
+    outdirMin: 512000
+    description: "the process requires at least 4G of RAM"
+
+inputs:
+  - id: "#bam_input"
+    type: File
+    description: "The BAM file used as input, it must be sorted."
+    inputBinding:
+      position: 1
+
+outputs:
+  - id: "#bamstats_report"
+    type: File
+    outputBinding:
+      glob: bamstats_report.zip
+    description: "A zip file that contains the HTML report and various graphics."
+
+baseCommand: ["bash", "/usr/local/bin/bamstats"]

README.md

@@ -1,2 +1,60 @@
 # dockstore-tool-bamstats
-A repo for the BAMStats command
+
+A repo for the `Dockerfile` to create a Docker image for the BAMStats command. Also contains the
+`Dockstore.yml` which is used by the [Dockstore](http://www.dockstore.org) to register
+this container and describe how to call BAMStats for the community.
+
+## Building Manually
+
+Normally you would let [Quay.io](http://quay.io) build this.  But, if you need to build
+manually you would execute:
+
+    docker build -t briandoconnor/dockstore-tool-bamstats:1.25 .
+
+## Running Manually
+
+```
+$ wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
+$ docker run -it -v `pwd`/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam:/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam briandoconnor/dockstore-tool-bamstats:1.25
+
+# within the docker container
+$ java -Xmx7g -jar /opt/BAMStats-1.25/BAMStats-1.25.jar -i /NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam -o test.html -v html
+```
+
+## Running Through the Dockstore Descriptor Launcher
+
+This tool can be found at the [Dockstore Descriptor](https://github.com/CancerCollaboratory/dockstore-descriptor) git repo.  It lets you run a Docker container with a CWL descriptor locally, using Docker and the CWL command
+line utility.  This is great for testing.
+
+### Create Config File
+
+Call it `launcher.ini`:
+
+```
+working-directory=./datastore/
+```
+
+### Make a Parameters JSON
+
+This is the parameterization of the BAM stat tool:
+
+```
+{
+  "bam_input": {
+        "class": "File",
+        "path": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam"
+    },
+    "bamstats_report": {
+        "class": "File",
+        "path": "s3://oicr.temp/testing-launcher/bamstats_report.zip"
+    }
+}
+```
+
+### Run with Launcher
+
+Run it using Java, make sure you have the dependencies installed for the Launcher, see the link above:
+
+```
+$ java -cp uber-io.github.collaboratory.launcher-1.0.2-SNAPSHOT.jar io.github.collaboratory.LauncherCWL --config launcher.ini --descriptor Dockstore.cwl --job sample_configs.json
+```

bin/bamstats

@@ -0,0 +1,5 @@
+#!/bin/bash
+set -euf -o pipefail
+
+java -Xmx4g -jar /opt/BAMStats-1.25/BAMStats-1.25.jar -i $1 -o bamstats_report.html -v html
+zip -r bamstats_report.zip bamstats_report.html bamstats_report.html.data

launcher.ini

@@ -0,0 +1 @@
+working-directory=./datastore/

node-engine.cwl

@@ -0,0 +1,5 @@
+class: ExpressionEngineRequirement
+requirements:
+  - class: DockerRequirement
+    dockerPull: commonworkflowlanguage/nodejs-engine
+engineCommand: cwlNodeEngine.js

sample_configs.json

@@ -0,0 +1,10 @@
+{
+  "bam_input": {
+        "class": "File",
+        "path": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam"
+    },
+    "bamstats_report": {
+        "class": "File",
+        "path": "s3://oicr.temp/testing-launcher/bamstats_report.zip"
+    }
+}