Add a 'distribution' module to create assemblies

o Moves the maven-assembly-plugin from adam-cli to the
  new distribution module
o Updates the adam-submit and friends to work from source
  or binary distributions
o Generates docs and adds them to the distribution
o Adds LICENSE, NOTICE.txt, CHANGES.md, etc to distribution

adam-cli/pom.xml

@@ -33,23 +33,6 @@
           </execution>
         </executions>
       </plugin>
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-assembly-plugin</artifactId>
-        <configuration>
-          <descriptors>
-            <descriptor>src/main/assembly/assembly.xml</descriptor>
-          </descriptors>
-        </configuration>
-        <executions>
-          <execution>
-            <phase>package</phase>
-            <goals>
-              <goal>single</goal>
-            </goals>
-          </execution>
-        </executions>
-      </plugin>
       <!-- disable surefire -->
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>

bin/adam-submit

@@ -18,26 +18,34 @@
 #
 
 # Figure out where ADAM is installed
-ADAM_REPO="$(cd `dirname $0`/..; pwd)"
+SCRIPT_DIR="$(cd `dirname $0`/..; pwd)"
 
 # Get list of required jars for ADAM
-ADAM_JARS=$("$ADAM_REPO"/bin/compute-adam-jars.sh)
+ADAM_JARS=$("$SCRIPT_DIR"/bin/compute-adam-jars.sh)
+
+# Binary distribution
+REPO_DIR="$SCRIPT_DIR/repo"
+if [ ! -d "$REPO_DIR" ]; then
+# Fallback to source directory
+REPO_DIR="$SCRIPT_DIR/adam-cli/target/appassembler/repo/"
+fi
 
 # Find the ADAM CLI jar
-num_versions=$(ls "$ADAM_REPO"/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli | wc -l)
+CLI_DIR="$REPO_DIR/org/bdgenomics/adam/adam-cli"
+num_versions=$(ls "$CLI_DIR" | wc -l)
 if [ "$num_versions" -eq "0" ]; then
-  echo "Failed to find adam-cli jar in $ADAM_REPO/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli"
+  echo "Failed to find adam-cli jar in $CLI_DIR"
   echo "You need to build ADAM before running this program."
   exit 1
 fi
 if [ "$num_versions" -gt "1" ]; then
-  versions_list=$(ls "$ADAM_REPO"/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli)
-  echo "Found multiple ADAM CLI versions in $ADAM_REPO/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli:"
+  versions_list=$(ls "$CLI_DIR")
+  echo "Found multiple ADAM CLI versions in $CLI_DIR:"
   echo "$versions_list"
   echo "Please remove all but one."
   exit 1
 fi
-ADAM_CLI_JAR="$(ls "$ADAM_REPO"/adam-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli/*/adam-cli-*.jar)"
+ADAM_CLI_JAR=$(ls $CLI_DIR/*/adam-cli-*.jar)
 
 # Find spark-submit script
 if [ -z "$SPARK_HOME" ]; then

bin/compute-adam-classpath.sh

@@ -18,16 +18,25 @@
 #
 
 # Figure out where ADAM is installed
-ADAM_REPO="$(cd `dirname $0`/..; pwd)"
+SCRIPT_DIR="$(cd `dirname $0`/..; pwd)"
 
-# Next three commands set CLASSPATH like appassembler
-BASEDIR="$ADAM_REPO"/adam-cli/target/appassembler
-REPO="$BASEDIR"/repo
-if [ ! -f "$BASEDIR"/bin/adam ]; then
+# Setup CLASSPATH like appassembler
+
+# Assume we're running in a binary distro
+ADAM_CMD="$SCRIPT_DIR/bin/adam"
+REPO="$SCRIPT_DIR/repo"
+
+# Fallback to source repo
+if [ ! -f $ADAM_CMD ]; then
+ADAM_CMD="$SCRIPT_DIR/adam-cli/target/appassembler/bin/adam"
+REPO="$SCRIPT_DIR/adam-cli/target/appassembler/repo"
+fi
+
+if [ ! -f "$ADAM_CMD" ]; then
   echo "Failed to find appassembler scripts in $BASEDIR/bin"
   echo "You need to build ADAM before running this program"
   exit 1
 fi
-eval $(cat "$BASEDIR"/bin/adam | grep "^CLASSPATH")
+eval $(cat "$ADAM_CMD" | grep "^CLASSPATH")
 
 echo "$CLASSPATH"

distribution/pom.xml

@@ -0,0 +1,53 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>org.bdgenomics.adam</groupId>
+        <artifactId>adam-parent</artifactId>
+        <version>0.14.1-SNAPSHOT</version>
+        <relativePath>../pom.xml</relativePath>
+    </parent>
+
+    <artifactId>adam-distribution</artifactId>
+    <packaging>pom</packaging>
+    <name>ADAM: Distribution</name>
+    <build>
+        <plugins>
+            <plugin>
+                <artifactId>exec-maven-plugin</artifactId>
+                <groupId>org.codehaus.mojo</groupId>
+                <executions>
+                    <execution>
+                        <id>Generate Documentation</id>
+                        <phase>generate-sources</phase>
+                        <goals>
+                            <goal>exec</goal>
+                        </goals>
+                        <configuration>
+                            <workingDirectory>${project.basedir}/../docs</workingDirectory>
+                            <executable>./build.sh</executable>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <configuration>
+                    <descriptors>
+                        <descriptor>src/main/assembly/assembly.xml</descriptor>
+                    </descriptors>
+                </configuration>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>single</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+</project>

distribution/src/main/assembly/assembly.xml

@@ -0,0 +1,67 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
+          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+          xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
+    <id>bin</id>
+    <formats>
+        <format>tar.gz</format>
+        <format>tar.bz2</format>
+        <format>zip</format>
+    </formats>
+    <fileSets>
+        <fileSet>
+            <directory>../</directory>
+            <includes>
+                <include>LICENSE.txt</include>
+                <include>NOTICE.txt</include>
+                <include>CHANGES.md</include>
+                <include>CONTRIBUTING.md</include>
+                <include>README.md</include>
+            </includes>
+            <outputDirectory>.</outputDirectory>
+        </fileSet>
+        <fileSet>
+            <directory>../adam-cli/target/appassembler/bin</directory>
+            <outputDirectory>bin</outputDirectory>
+            <excludes>
+                <exclude>*.bat</exclude>
+            </excludes>
+            <directoryMode>0755</directoryMode>
+            <fileMode>0755</fileMode>
+        </fileSet>
+        <fileSet>
+            <directory>../adam-cli/target/appassembler/bin</directory>
+            <outputDirectory>bin</outputDirectory>
+            <includes>
+                <include>*.bat</include>
+            </includes>
+            <directoryMode>0755</directoryMode>
+            <fileMode>0644</fileMode>
+        </fileSet>
+        <fileSet>
+            <directory>../adam-cli/target/appassembler/repo</directory>
+            <outputDirectory>repo</outputDirectory>
+            <directoryMode>0755</directoryMode>
+            <fileMode>0644</fileMode>
+        </fileSet>
+        <fileSet>
+            <directory>../bin</directory>
+            <outputDirectory>bin</outputDirectory>
+            <directoryMode>0755</directoryMode>
+            <fileMode>0755</fileMode>
+        </fileSet>
+        <fileSet>
+            <directory>../docs/output</directory>
+            <outputDirectory>docs</outputDirectory>
+            <directoryMode>0755</directoryMode>
+            <fileMode>0644</fileMode>
+        </fileSet>
+    </fileSets>
+    <!--
+      <dependencySets>
+        <dependencySet>
+          <outputDirectory>repo</outputDirectory>
+        </dependencySet>
+      </dependencySets>
+    -->
+</assembly>

docs/build.sh

@@ -3,6 +3,7 @@
 git_version=$(git rev-parse --short HEAD)
 
 output_dir="output"
+rm $output_dir/* 2>/dev/null
 pdf_output="$output_dir/ADAM_v$git_version.pdf"
 html_output="$output_dir/ADAM_v$git_version.html"
 date_str=$(date '+%Y-%m-%d')
@@ -12,6 +13,12 @@ date="$date_str git:$git_version"
 author="http://bdgenomics.org/"
 highlight_style="tango"
 
+which pandoc >/dev/null 2>&1
+if [ $? -ne "0" ]; then
+	echo "WARNING! Pandoc not found on path. Documentation will not be generated!"
+	exit 0
+fi
+
 # Generate a PDF of the docs
 pandoc -N --template=template.tex \
 --highlight-style "$highlight_style" \

pom.xml

@@ -32,6 +32,8 @@
     <module>adam-core</module>
     <module>adam-apis</module>
     <module>adam-cli</module>
+    <!-- distribution should be last -->
+    <module>distribution</module>
   </modules>
 
   <licenses>

scripts/jenkins-test

@@ -61,7 +61,7 @@ popd
 
 pushd "$PROJECT_ROOT"
 ./scripts/format-source
-if grep --quiet "dirty" <(git describe --dirty --tags)
+if test -n "$(git status --porcelain)"
 then
         echo "Please run './scripts/format-source'"
         exit 1