From 93dc2cdc70f22835144a3cc96fcc9a034e610df6 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 15 Jun 2009 00:52:48 +0000
Subject: [PATCH] Start of a 'package' format for xml files which should be
 distributed together. Uses xslt scripts to transform packages into build
 scripts.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1005 348d0f76-0448-11de-a6fe-93d51630548a
---
 packages/CreatePackager.xsl          | 83 ++++++++++++++++++++++++++++
 packages/ReadQualityRecalibrator.xml | 20 +++++++
 2 files changed, 103 insertions(+)
 create mode 100644 packages/CreatePackager.xsl
 create mode 100644 packages/ReadQualityRecalibrator.xml

diff --git a/packages/CreatePackager.xsl b/packages/CreatePackager.xsl
new file mode 100644
index 000000000..3fa71070e
--- /dev/null
+++ b/packages/CreatePackager.xsl
@@ -0,0 +1,83 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
+
+<xsl:template match="package">
+  <xsl:output method="xml" indent="yes"/>
+
+  <xsl:variable name="project.name" select="name" />
+
+  <xsl:variable name="ant.basedir" select="'${basedir}'" />
+  <xsl:variable name="sting.dir" select="'${sting.dir}/'" />
+  <xsl:variable name="staging.dir" select="'${sting.dir}/staging'" />
+  <xsl:variable name="package.dir" select="'${package.dir}/'" />
+  <xsl:variable name="resources.dir" select="'${package.dir}/resources'" />
+
+  <project name="{$project.name}" default="package" basedir="..">
+    <property name="sting.dir" value="{$ant.basedir}" />
+    <property name="package.dir" value="{concat($ant.basedir,'/packages/',$project.name)}" />
+
+    <target name="package">
+      <mkdir dir="{$package.dir}"/>
+      <mkdir dir="{$resources.dir}"/>
+      <copy todir="{$resources.dir}">
+        <classfileset dir="{$staging.dir}">
+          <root classname="{main-class}"/>
+        <xsl:for-each select="dependencies/class">
+          <root classname="{current()}" />
+        </xsl:for-each>
+        </classfileset>
+      </copy>
+      <xsl:for-each select="scripts/file">
+        <xsl:variable name="short.name">
+          <xsl:call-template name="get-short-name">
+            <xsl:with-param name="string" select="." />
+          </xsl:call-template>
+        </xsl:variable>
+        <xsl:variable name="full.path">
+          <xsl:call-template name="get-full-path">
+            <xsl:with-param name="working-dir" select="$sting.dir"/>
+            <xsl:with-param name="file" select="."/>
+          </xsl:call-template>
+        </xsl:variable>
+        <symlink link="{concat($package.dir,$short.name)}" resource="{$full.path}" overwrite="true" />
+      </xsl:for-each>
+      <xsl:for-each select="resources/file">
+        <xsl:variable name="short.name">
+          <xsl:call-template name="get-short-name">
+            <xsl:with-param name="string" select="." />
+          </xsl:call-template>
+        </xsl:variable>
+        <xsl:variable name="full.path">
+          <xsl:call-template name="get-full-path">
+            <xsl:with-param name="working-dir" select="$sting.dir"/>
+            <xsl:with-param name="file" select="."/>
+          </xsl:call-template>
+        </xsl:variable>
+        <symlink link="{concat($resources.dir,'/',$short.name)}" resource="{$full.path}" overwrite="true" />
+      </xsl:for-each>
+    </target>
+  </project>
+</xsl:template>
+
+<xsl:template name="get-short-name">
+  <xsl:param name="string"/>
+  <xsl:choose>
+    <xsl:when test="contains($string,'/')">
+      <xsl:call-template name="get-short-name">
+        <xsl:with-param name="string" select="substring-after($string,'/')" />
+      </xsl:call-template>
+    </xsl:when>
+    <xsl:otherwise><xsl:value-of select="$string"/></xsl:otherwise>
+  </xsl:choose>    
+</xsl:template>
+
+<xsl:template name="get-full-path">
+  <xsl:param name="working-dir"/>
+  <xsl:param name="file"/>
+  <xsl:choose>
+    <xsl:when test="starts-with($file,'/')"><xsl:value-of select="$file"/></xsl:when>
+    <xsl:otherwise><xsl:value-of select="concat($working-dir,$file)"/></xsl:otherwise>
+  </xsl:choose>
+</xsl:template>
+
+</xsl:stylesheet>
diff --git a/packages/ReadQualityRecalibrator.xml b/packages/ReadQualityRecalibrator.xml
new file mode 100644
index 000000000..02b23face
--- /dev/null
+++ b/packages/ReadQualityRecalibrator.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<package>
+  <name>ReadQualityRecalibrator</name>
+  <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+  <dependencies>
+    <class>org.broadinstitute.sting.playground.gatk.walkers.CovariateCounterWalker</class>
+    <class>org.broadinstitute.sting.playground.gatk.walkers.LogisticRecalibrationWalker</class>
+  </dependencies>
+  <scripts>
+    <file>python/RecalQual.py</file>
+    <file>python/LogisticRegressionByReadGroup.py</file>
+  </scripts>
+  <resources>
+    <file>R/logistic_regression.R</file>
+    <file>/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod</file>
+    <file>/broad/1KG/reference/human_b36_both.fasta</file>
+    <file>/broad/1KG/reference/human_b36_both.dict</file>
+    <file>/broad/1KG/reference/human_b36_both.fasta.fai</file>
+  </resources>
+</package>