Revert "Update README.md"

This reverts commit fbf5aca.

README.md

@@ -1,12 +1,15 @@
 [![Docker Repository on Quay.io](https://quay.io/repository/collaboratory/dockstore-tool-bamstats/status "Docker Repository on Quay.io")](https://quay.io/repository/collaboratory/dockstore-tool-bamstats)
+[![Build Status](https://travis-ci.org/CancerCollaboratory/dockstore-tool-bamstats.svg)](https://travis-ci.org/CancerCollaboratory/dockstore-tool-bamstats)
 
 # dockstore-tool-bamstats
 
-A repo for the `Dockerfile` to create a Docker image 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](https://www.dockstore.org) to register
+this container and describe how to call BAMStats for the community.
 
 ## Validation 
 
-The CWL version of this tool has been validated as a CWL draft-3 and v1.0 CommandLineTool. 
+This tool has been validated as a CWL draft-3 and v1.0 CommandLineTool. 
 
 Versions that we tested with are the following 
 ```
@@ -30,13 +33,17 @@ manually you would execute:
 
 ```
 $ wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
-$ docker run -w="/home/ubuntu" -v `pwd`:/home/ubuntu --user `echo $UID`:1000 quay.io/collaboratory/dockstore-tool-bamstats:1.25-6 bamstats 4 NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
+$ docker run -it -v `pwd`/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam:/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam collaboratory/dockstore-tool-bamstats:1.25-3
+
+# within the docker container
+$ /usr/local/bin/bamstats 4 /NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
 ```
-You'll then see a file, `bamstats_report.zip`. Using the command above, it will automatically be mounted out of the container.
+You'll then see a file, `bamstats_report.zip`, in the current directory, that's the report file. You can use `-v` to mount the result out of the container.
 
 ## Running Through the Dockstore CLI
 
-This tool can be found at [Dockstore](https://dockstore.org). The [Dockstore CLI](https://github.com/dockstore/dockstore-cli) is a powerful tool for testing, letting you run a Docker container with a CWL/WDL descriptor locally, using Docker and the CWL/WDL command line utility.
+This tool can be found at the [Dockstore](https://dockstore.org), login with your GitHub account and follow the 
+directions to setup the CLI.  It lets you run a Docker container with a CWL/WDL descriptor locally, using Docker and the CWL/WDL command line utility.  This is great for testing.
 
 ### With CWL