# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1369879826 14400
# Node ID d529eff9883480dc959793d4b723ef61ec4d4780
# Parent  28fda763185755ff1d5b8b8adb0463849d600b1b
tool dependencies for automated sra_sdk download and compilation

diff -r 28fda7631857 -r d529eff98834 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed May 29 22:10:26 2013 -0400
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="sra_toolkit" version="2.3.2-4">
+    <install version="1.0">
+      <actions>
+	<action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.2-4/sra_sdk-2.3.2-4.tar.gz</action>
+	<action type="shell_command">make OUTDIR=$INSTALL_DIR out</action>
+	<action type="shell_command">make release</action>
+	<action type="shell_command">make</action>
+	<action type="shell_command">cd $INSTALL_DIR</action>
+	<action type="shell_command">if [[ $(uname -m) =~ x86_64 ]]; then ln -s bin64 bin; elif [[ $(uname -m) =~ i.86 ]]; then ln -s bin32 bin; fi</action>
+	<action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
+      </actions>
+    </install>
+    <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. Various tools for working with SRA from NCBI.
+This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 32 and 64 bit architectures.
+Build Requirements:
+  ar 
+  bash
+  make
+  gcc, g++
+  libxml2
+  libcurl
+  zlib
+    </readme>
+  </package>
+</tool_dependency>