# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1427738776 14400
# Node ID 91558de676f4622a077513add9589c66b4160c49
# Parent  16f96ab0196b2942a97498c83fcd2b7f4323cd1e
Update to latest toolkit version - fix installation issues.

diff -r 16f96ab0196b -r 91558de676f4 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 03 13:40:03 2015 -0500
+++ b/tool_dependencies.xml	Mon Mar 30 14:06:16 2015 -0400
@@ -1,37 +1,52 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="sra_toolkit" version="2.4.3">
+  <package name="sra_toolkit" version="2.4.5">
     <install version="1.0">
       <actions>
-        <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current.version</action>
-        <action type="shell_command">make release</action>
-        <action type="shell_command">make static</action>
-        <action type="shell_command">make</action>
-        <action type="make_directory">$INSTALL_DIR/bin</action>
-        <action type="make_directory">$INSTALL_DIR/ncbi</action>
-        <action type="make_directory">$INSTALL_DIR/ncbi/public</action>
-        <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg</action>
-        <action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action>
-        <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
+        <action type="set_environment">
+          <environment_variable name="NCBI" action="set_to">$PWD/ncbi</environment_variable>
+          <environment_variable name="BUILD" action="set_to">$PWD/build</environment_variable>
+          <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/lib64</environment_variable>
+          <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/lib</environment_variable>
+        </action>
+        <action type="make_directory">$BUILD</action>
+        <action type="make_directory">$NCBI</action>
+        <action type="change_directory">$NCBI</action>
+        <action type="shell_command">git clone https://github.com/ncbi/sra-tools.git</action>
+        <action type="shell_command">git clone https://github.com/ncbi/ncbi-vdb.git</action>
+        <action type="shell_command">git clone https://github.com/ncbi/ngs.git</action>
+        <action type="change_directory">$NCBI/ncbi-vdb</action>
+        <action type="shell_command">git checkout bf5ffdd</action>
+        <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action>
+        <action type="change_directory">$NCBI/ngs</action>
+        <action type="shell_command">git checkout 3a7a0ed</action>
+        <action type="change_directory">$NCBI/ngs/ngs-sdk</action>
+        <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD</action>
+        <action type="change_directory">$NCBI/sra-tools</action>
+        <action type="shell_command">git checkout 4ef7ea0</action>
+        <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$BUILD --with-ncbi-vdb-build=$BUILD --with-ncbi-vdb-sources=$NCBI/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR --with-magic-prefix=/dev/null</action>
+        <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</action>
       </actions>
     </install>
-    <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
+    <readme>
+Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
 download of a large SRA data set.
 
 Build Requirements:
-  ar
-  bash
-  make
-  gcc, g++
-  libxml2
-  libcurl4
-  zlib
+  - make
+  - git
+  - gcc
+  - g++
+  - libxml2
+  - libcurl4
+  - zlib
 
 On a debian based Linux OS use:
 
   apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
+
     </readme>
   </package>
 </tool_dependency>