Improved README, works with embedded Docker Compose

README.md

@@ -63,22 +63,32 @@ Once GaPTools is setup, to execute it on the included sample study, run the belo
 ./dbgap-docker.bash -i ./input_files/1000_Genomes_Study/ -o ./output_files/1000_Genomes_Study -m ./input_files/1000_Genomes_Study/metadata.json up
 ```
 
-GaPTools uses Apache Airflow behind the scenes as the workflow orchestrator to perform all the validation tasks. To view the validation results of the dbGaP validation tool, browse to the following URL:
+GaPTools uses [Apache Airflow](https://airflow.apache.org/) behind the scenes as the workflow orchestrator to perform all the validation tasks. To view the validation results of the dbGaP validation tool, browse to the following URL:
 
 ```
 http://<your_docker_host_ip>:8080
 ```  
 
+If you are running this locally on a workstation, this can often be found at http://localhost:8080. 
+
+
 At the end of the workflow, the output files will be created under the specified output directory.
+
 ## Usage
 
 To use GaPTools for your study, modify the above command and pass as input parameters:
 
-__-i__ -- path to the input files for your study
+- __`-i path/to/INPUT_DIR`__ -- path to the input files for your study (may also use `--input [...]` on Linux OS's)
+
+- __`-o path/to/OUTPUT_DIR`__ -- path where output files should be generated (may also use `--output [...]` on Linux OS's)
+
+- __`-m path/to/metadata.json`__ -- path to the manifest file for your study (may also use `--manifest [...]` on Linux OS's)
 
-__-o__ -- path where output files should be generated
+- __`-h`__ -- print full usage information at the command line (may also use `--help` on Linux OS's)
+
+### Note on macOS
 
-__-m__ -- path to the manifest file for your study
+On macOS, only the short versions of the command line options are supported.  (`-i`, `-o`, `-m`, `-h`)
 
 ## Stop Docker Containers
 
@@ -88,4 +98,4 @@ Once your study is processed, run the below command to stop the GaPTools service
 ```
 
 ## Contact
-If you have any questions or to report any issues, please contact us at: [dbgap-help@ncbi.nlm.nih.gov](dbgap-help@ncbi.nlm.nih.gov)
+If you have any questions or to report any issues, please contact us at: [dbgap-help@ncbi.nlm.nih.gov](mailto:dbgap-help@ncbi.nlm.nih.gov)

dbgap-docker.bash

@@ -5,18 +5,18 @@
 #================================================================
 #% SYNOPSIS
 #+    ${SCRIPT_NAME} [-h] [-i, --input [input directory]]
-#+                     [-o, --output [output directory]] 
+#+                     [-o, --output [output directory]]
 #+                     [-m, --manifest [manifest file]]
 #+                     [up|down]
 #+
 #% DESCRIPTION
 #%    This script runs GaPTools to validate data files
-#%    to be submitted to dbGaP. It loads a docker-compose
+#%    to be submitted to dbGaP. It loads a Docker Compose
 #%    file and runs required docker containers.
 #%
 #%
 #% OPTIONS
-#%    -i, --input                   Input directory containing the 
+#%    -i, --input                   Input directory containing the
 #%                                  data files to be validated.
 #%    -o, --output                  Output directory
 #%    -m, --manifest                Manifest file with metadata
@@ -31,6 +31,9 @@
 #%    docker
 #%    docker-compose
 #%
+#% NOTES
+#%    macOS and other BSD-based systems do not support long options (--help, etc)
+#%    Use the short option equivalents (-i, -o, -m, -h)
 #%
 #================================================================
 # END_OF_HEADER
@@ -53,12 +56,22 @@ OPTIONS=ht:i:o:m:
 LONGOPTS=help,input:,output:,manifest:
 
 # pass arguments only via   -- "$@"   to separate them correctly
-! PARSED=$(getopt --options=$OPTIONS --longoptions=$LONGOPTS --name "$0" -- "$@")
+if [[ "$OSTYPE" == "darwin"* ]]; then
+   # macOS uses the BSD getopt, which does not support long options.
+   ! PARSED=$(getopt $OPTIONS "$@")
+else
+   ! PARSED=$(getopt --options=$OPTIONS --longoptions=$LONGOPTS --name "$0" -- "$@")
+fi
+
 if [[ ${PIPESTATUS[0]} -ne 0 ]]; then
     # e.g. return value is 1
     #  then getopt has complained about wrong arguments to stdout
     echo "Wrong number/type of arguments"
     usage
+    if [[ "$OSTYPE" == "darwin"* ]]; then
+        # macOS uses the BSD getopt, which does not support long options.
+        echo "WARNING:  On macOS:  long options (e.g. '--help') are not supported."
+    fi
     exit 2
 fi
 # read getopt output to handle the quoting:
@@ -72,7 +85,7 @@ while true; do
             exit
             ;;
         -i|--input)
-            INPUT_DIR="$2" 
+            INPUT_DIR="$2"
             INPUT_DIR="$(echo -e "${INPUT_DIR}" | tr -d '[[:space:]]')"
             if [ -z "$INPUT_DIR" ]; then
                echo $INPUT_DIR "Please provide the input directory"
@@ -84,10 +97,10 @@ while true; do
                usage
                exit 2
             fi
-            shift 2 
+            shift 2
             ;;
         -o|--output)
-            OUTPUT_DIR="$2" 
+            OUTPUT_DIR="$2"
             OUTPUT_DIR="$(echo -e "${OUTPUT_DIR}" | tr -d '[[:space:]]')"
             if [ -z "$OUTPUT_DIR" ]; then
                echo $OUTPUT_DIR "Please provide the output directory"
@@ -98,11 +111,11 @@ while true; do
                echo $OUTPUT_DIR "Please provide the output directory"
                usage
                exit 2
-            fi 
+            fi
             shift 2
             ;;
         -m| --manifest)
-            MANIFEST="$2" 
+            MANIFEST="$2"
             MANIFEST="$(echo -e "${MANIFEST}" | tr -d '[[:space:]]')"
             if [ -z "$MANIFEST" ]; then
                echo $MANIFEST "Please provide full path to the manifest file"
@@ -113,7 +126,7 @@ while true; do
                echo $MANIFEST "Please provide full path to the manifest file"
                usage
                exit 2
-            fi 
+            fi
             shift 2
             ;;
         --)
@@ -128,6 +141,16 @@ while true; do
     esac
 done
 
+if command -v docker-compose > /dev/null ; then
+   DOCKER_COMPOSE_COMMAND="docker-compose"
+elif docker compose version 2>&1 > /dev/null ; then
+   DOCKER_COMPOSE_COMMAND="docker compose"
+else
+   echo "Docker Compose not found"
+   usage
+   exit 2
+fi
+
 ##################
 # Verify up/down arguments were supplied properly
 ##################
@@ -144,11 +167,11 @@ if ! [[ "${DSTATE}" =~ ^(up|down)$ ]]; then
 fi
 
 #########################
-# Run the docker-compose commands to bring the environment down
+# Run the $DOCKER_COMPOSE_COMMAND commands to bring the environment down
 # Skips the rest of the validation and exit the script
 #########################
 if [ $DSTATE == "down" ]; then
-   docker-compose -f docker-compose-CeleryExecutor.yml down
+   $DOCKER_COMPOSE_COMMAND -f docker-compose-CeleryExecutor.yml down
    exit
 fi
 
@@ -204,7 +227,7 @@ if [ ! -f "$MANIFEST" ]; then
 fi
 
 ########################
-# Create a .env file to be used by docker-compose
+# Create a .env file to be used by $DOCKER_COMPOSE_COMMAND
 ########################
 echo "OUTPUT_VOL=${OUTPUT_DIR}" > .env
 echo "INPUT_VOL=${INPUT_DIR}" >> .env
@@ -250,15 +273,15 @@ docker_check() {
             return 0
          fi
       done < <(docker ps)
-   return 1 
+   return 1
 }
 
 #########################
-# Run the docker-compose commands to bring the environment up
+# Run the $DOCKER_COMPOSE_COMMAND commands to bring the environment up
 #########################
 if [ $DSTATE == "up" ]; then
    docker pull ncbi/gaptools:latest
-   docker-compose -f docker-compose-CeleryExecutor.yml up -d
+   $DOCKER_COMPOSE_COMMAND -f docker-compose-CeleryExecutor.yml up -d
    i=0
    while ! docker_check
    do
@@ -268,12 +291,12 @@ if [ $DSTATE == "up" ]; then
          echo "Timed out waiting for webserver to start"
          echo "Check the docker container logs by executing the command \"docker logs [container_name]\""
          echo "E.g. \"docker logs gaptools_webserver_1\""
-         echo 
+         echo
          exit 2
       fi
       sleep 10
    done
-   
+
    echo ""
    echo "The airflow server has started on port 8080. Visit "
    echo "http://<your_docker_host_ip>:8080"