diff tool_dependencies.xml @ 2:293927a46697

Move from test tool shed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 25 21:08:40 2013 -0400
@@ -0,0 +1,37 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="sra_toolkit" version="2.3.3-3">
+    <install version="1.0">
+      <actions>
+        <action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.3-3/sra_sdk-2.3.3-3.tar.gz</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>
+      </actions>
+    </install>
+    <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
+  
+On a debian based Linux OS use:
+
+  apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
+    </readme>
+  </package>
+</tool_dependency>