Examples from README.MD added

app/conf/resource-config.json

@@ -21,6 +21,9 @@
     }, 
     {
       "pattern":"\\Qtemplates/spack/dockerfile-spack-file.txt\\E"
+    },
+    {
+      "pattern":"\\Qio/seqera/wavelit/examples.txt\\E"
     }
   ]},
   "bundles":[]

app/src/main/java/io/seqera/wavelit/App.java

@@ -20,9 +20,11 @@
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.time.OffsetDateTime;
 import java.util.Arrays;
 import java.util.Base64;
@@ -57,7 +59,11 @@
 /**
  * Wavelit main class
  */
-@Command(name = "wavelit", description = "Wave command line tool", mixinStandardHelpOptions = true, versionProvider = CliVersionProvider.class, usageHelpAutoWidth = true)
+@Command(name = "wavelit",
+        description = "Wave command line tool",
+        mixinStandardHelpOptions = true,
+        versionProvider = CliVersionProvider.class,
+        usageHelpAutoWidth = true)
 public class App implements Runnable {
 
     private static final String DEFAULT_TOWER_ENDPOINT = "https://api.tower.nf";
@@ -156,6 +162,11 @@ public static void main(String[] args) {
         try {
             final App app = new App();
             final CommandLine cli = new CommandLine(app);
+
+            // add examples in help
+            CommandLine.Model.UsageMessageSpec usageMessageSpec = cli.getCommandSpec().usageMessage();
+            usageMessageSpec.footer(loadExamples("examples.txt"));
+
             final CommandLine.ParseResult result = cli.parseArgs(args);
             if( result.matchedArgs().size()==0 || result.isUsageHelpRequested() ) {
                 cli.usage(System.out);
@@ -177,6 +188,19 @@ else if( result.isVersionHelpRequested() ) {
         }
     }
 
+    private static String loadExamples(String exampleFile) {
+            try(InputStream inputStream = App.class.getResourceAsStream(exampleFile)) {
+                if (inputStream != null) {
+                    byte[] buffer = new byte[inputStream.available()];
+                    inputStream.read(buffer);
+                    return new String(buffer, StandardCharsets.UTF_8);
+                }
+            } catch (IOException e) {
+                return e.getMessage();
+            }
+        return "nothing";
+    }
+
     protected void setLogLevel() {
         if( !isEmpty(logLevel) ) {
             Logger root = (Logger) LoggerFactory.getLogger(Logger.ROOT_LOGGER_NAME);

app/src/main/resources/io/seqera/wavelit/examples.txt

@@ -0,0 +1,45 @@
+Examples
+
+Augment a container image
+
+1. Create a directory holding the files to be added to your container:
+
+    mkdir -p new-layer/usr/local/bin
+    printf 'echo Hello world!' > new-layer/usr/local/bin/hello.sh
+    chmod +x new-layer/usr/local/bin/hello.sh
+
+2. Run the container via Wave
+
+    docker run $(wavelit -i alpine --layer new-layer) sh -c hello.sh
+
+Build a container with Dockerfile
+
+1. Create a Dockerfile for your container image:
+
+    cat << EOF > ./Dockerfile
+    FROM alpine
+    ADD hello.sh /usr/local/bin/
+    EOF
+
+2. Create the build context directory:
+
+    mkdir -p build-context/
+    printf 'echo Hello world!' > build-context/hello.sh
+    chmod +x build-context/hello.sh
+
+3. Build and run the container on the fly:
+
+    docker run $(wavelit -f Dockerfile --context build-context) sh -c hello.sh
+
+Build a Conda multi-packages container
+
+    docker run $(wavelit --conda-package bamtools=2.5.2 --conda-package samtools=1.17) sh -c 'bamtools --version && samtools --version'
+
+Build a Conda package container arm64 architecture
+
+    docker run --platform linux/arm64 $(wavelit --conda-package fastp --platform linux/arm64) sh -c 'fastp --version'
+
+Build a Spack package container
+
+    docker run $(wavelit --spack-package cowsay) sh -c 'cowsay Hello world!'
+