[PacMin-16] Fix broken readme links, and other build cleanup.

.gitignore

@@ -1,21 +1,8 @@
-*.class
-*.log
-
-# sbt specific
-.cache/
-.history/
-.lib/
-dist/*
-target/
-lib_managed/
-src_managed/
-project/boot/
-project/plugins/project/
-
-# Scala-IDE specific
-.scala_dependencies
-.worksheet
-
-# Emacs
+*.pdf
+*.html
 *~
-*#*
+*#*
+*.log
+target
+build
+.DS_Store

README.md

@@ -47,23 +47,18 @@ Once this alias is in place, you can run adam by simply typing `pacmin` at the c
 
 # Getting In Touch
 
-## IRC Channel
-
-A lot of the developers are hanging on the [#adamdev](http://webchat.freenode.net/?channels=adamdev)
-freenode.net channel. Come join us and ask questions.
-
 # License
 
-PacMin is released under an [Apache 2.0 license](LICENSE.txt).
+PacMin is released under an [Apache 2.0 license](https://github.com/bigdatagenomics/PacMin/blob/master/LICENSE).
 
 # Distribution
 
-Snapshots of PacMin are available from the [Sonatype OSS](oss.sonatype.org) repository:
+Snapshots of PacMin are available from the [Sonatype OSS](https://oss.sonatype.org) repository:
 
 ```
 <groupId>org.bdgenomics.pacmin</groupId>
 <artifactId>pacmin-core</artifactId>
 <version>0.0.1-SNAPSHOT</version>
 ```
 
-Once we've got a release, we will publish to [Maven Central](search.maven.org).
+Once we've got a release, we will publish to [Maven Central](http://search.maven.org).

docs/.gitignore

@@ -0,0 +1,2 @@
+*.pdf
+*.html

docs/build.sh

@@ -0,0 +1,49 @@
+#/usr/bin/env bash
+
+git_version=$(git rev-parse --short HEAD)
+
+output_dir="."
+pdf_output="$output_dir/pacmin_v$git_version.pdf"
+html_output="$output_dir/pacmin_v$git_version.html"
+date_str=$(date '+%Y-%m-%d')
+
+title="PacMin User Guide"
+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
+which pandoc-citeproc >/dev/null 2>&1
+if [ $? -ne "0" ]; then
+	echo "WARNING! Pandoc-citeproc not found on path. Documentation will not be generated!"
+	exit 0
+fi
+
+# Generate a PDF of the docs
+pandoc -N --template=template.tex \
+--filter pandoc-citeproc \
+--highlight-style "$highlight_style" \
+--variable mainfont="Georgia" \
+--variable sansfont="Arial" \
+--variable monofont="Andale Mono" \
+--variable fontsize=10pt \
+--variable version=$git_version \
+--variable listings=true \
+--variable title="$title" \
+--variable date="$date" \
+--variable author="$author" \
+--toc \
+source/*.md -s -S -o $pdf_output
+
+# Generate HTML of the docs
+pandoc source/*.md -H style.css -s -S --toc \
+--filter pandoc-citeproc \
+--highlight-style "$highlight_style" \
+--variable title="$title" \
+--variable date="$date" \
+--variable author="$author" \
+-o $html_output

docs/source/01_intro.md

@@ -0,0 +1,6 @@
+# Introduction
+
+PacMin is a long read assembly tool built on top of the [ADAM](https://www.github.com/bigdatagenomics/adam)
+genomics analysis platform and [Apache Spark](http://spark.apache.org/), and is optimized for running distributed
+across a cluster, or on a single machine.
+

docs/source/02_installation.md

@@ -0,0 +1,35 @@
+# Installation
+
+## Building PacMin from Source
+
+You will need to have [Maven](http://maven.apache.org/) installed in order to build PacMin.
+
+> **Note:** The default configuration is for Hadoop 2.2.0. However, PacMin does not package
+> either Spark or Hadoop, and should not need to be rebuilt to run on different Spark (after 1.0.0)
+> or Hadoop versions.
+
+```
+$ git clone https://github.com/bigdatagenomics/PacMin.git
+$ cd PacMin
+$ export "MAVEN_OPTS=-Xmx512m -XX:MaxPermSize=128m"
+$ mvn clean package
+```
+
+## Running PacMin
+
+PacMin is packaged via [appassembler](http://mojo.codehaus.org/appassembler/appassembler-maven-plugin/)
+and packages all necessary dependencies _except for_ Spark and Hadoop, which must be present on the
+system (see below).
+
+You might want to add the following to your `.bashrc` to make running PacMin easier:
+
+```
+alias PacMin-submit="${PACMIN_HOME}/bin/pacmin-submit"
+```
+
+`$PACMIN_HOME` should be the path to where you have checked PacMin out on your local filesystem. 
+This alias wraps the `spark-submit` command to run PacMin. You'll need
+to have the Spark binaries on your system; prebuilt binaries can be downloaded from the
+[Spark website](http://spark.apache.org/downloads.html). If you do not have a cluster, we recommend using
+[Spark 1.2, and Hadoop 2.3 (CDH5)](http://d3kbcqa49mib13.cloudfront.net/spark-1.2.0-bin-hadoop2.3.tgz).
+

docs/source/90_help.md

@@ -0,0 +1,7 @@
+# Getting help
+
+PacMin is pre-alpha and is maintained by [Frank Austin Nothaft](mailto:fnothaft@berkeley.edu).
+
+## Gitter Channel
+
+Project developers congregate in the [ADAM Gitter channel](https://gitter.im/bigdatagenomics/adam).

docs/source/99_legal.md

@@ -0,0 +1,4 @@
+# Licensing
+
+PacMin is released under an [Apache 2.0 license](LICENSE.txt).
+

docs/style.css

@@ -0,0 +1,71 @@
+<style type="text/css">
+body {
+    margin: auto;
+    padding-right: 1em;
+    padding-left: 1em;
+    max-width: 60em; 
+    border-left: 1px solid black;
+    border-right: 1px solid black;
+    color: black;
+    font-family: Verdana, sans-serif;
+    font-size: 100%;
+    line-height: 140%;
+    color: #333; 
+}
+code {
+    font-family: monospace;
+}
+h1 a, h2 a, h3 a, h4 a, h5 a { 
+    text-decoration: none;
+    color: #000066; 
+}
+h1, h2, h3, h4, h5 { font-family: verdana;
+                     font-weight: bold;
+                     border-bottom: 1px dotted black;
+                     color: #000066; }
+h1 {
+        font-size: 130%;
+}
+
+h2 {
+        font-size: 110%;
+}
+
+h3 {
+        font-size: 95%;
+}
+
+h4 {
+        font-size: 90%;
+        font-style: italic;
+}
+
+h5 {
+
+        font-size: 90%;
+        font-style: italic;
+}
+
+h1.title {
+        font-size: 200%;
+        font-weight: bold;
+        padding-top: 0.2em;
+        padding-bottom: 0.2em;
+        text-align: left;
+        border: none;
+}
+
+dt code {
+        font-weight: bold;
+}
+dd p {
+        margin-top: 0;
+}
+
+#footer {
+        padding-top: 1em;
+        font-size: 70%;
+        color: gray;
+        text-align: center;
+        }
+</style>