# HG changeset patch
# User Matt Shirley <mdshw5@gmail.com>
# Date 1379377648 14400
# Node ID 04cc8176e86fd3e1a652e723cbb4ff0dd60307c3
# Parent  88a13a2fd23fb564e10b0e0be41683be697d6bcf
update to SRA toolkit 2.3.3-3

diff -r 88a13a2fd23f -r 04cc8176e86f fastq_dump.xml
--- a/fastq_dump.xml	Tue Sep 03 22:02:30 2013 -0400
+++ b/fastq_dump.xml	Mon Sep 16 20:27:28 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Extract reads" version="1.1.0">
+<tool id="fastq_dump" name="Extract reads" version="1.1.1">
   <description> from NCBI SRA.</description>
   <command>
     fastq-dump --log-level fatal 
@@ -112,7 +112,7 @@
     <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
   </stdio>
   <requirements>
-    <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
+    <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
   </requirements>
   <help>
     This tool extracts reads from SRA archives using fastq-dump. 
diff -r 88a13a2fd23f -r 04cc8176e86f sam_dump.xml
--- a/sam_dump.xml	Tue Sep 03 22:02:30 2013 -0400
+++ b/sam_dump.xml	Mon Sep 16 20:27:28 2013 -0400
@@ -88,7 +88,7 @@
     </data>
   </outputs>
   <requirements>
-    <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
+    <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
   </requirements>
   <help>
     This tool extracts reads from sra archives using sam-dump. 
diff -r 88a13a2fd23f -r 04cc8176e86f sra_pileup.xml
--- a/sra_pileup.xml	Tue Sep 03 22:02:30 2013 -0400
+++ b/sra_pileup.xml	Mon Sep 16 20:27:28 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="sra_pileup" name="Generate pileup format" version="1.0.1">
+<tool id="sra_pileup" name="Generate pileup format" version="1.1.1">
   <description> from NCBI sra.</description>
   <command>sra-pileup --log-level fatal 
     #if str( $region ) != "":
@@ -40,7 +40,7 @@
     <data format="pileup" name="output"/>
   </outputs>
   <requirements>
-    <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
+    <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
   </requirements>
   <help>
     This tool produces pileup format from sra archives using sra-pileup. 
diff -r 88a13a2fd23f -r 04cc8176e86f tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 03 22:02:30 2013 -0400
+++ b/tool_dependencies.xml	Mon Sep 16 20:27:28 2013 -0400
@@ -1,18 +1,18 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="sra_toolkit" version="2.3.2-4">
+  <package name="sra_toolkit" version="2.3.3-3">
     <install version="1.0">
       <actions>
-	<action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.2-4/sra_sdk-2.3.2-4.tar.gz</action>
-	<action type="shell_command">make release</action>
-	<action type="shell_command">make static</action>
-	<action type="shell_command">make</action>
-	<action type="make_directory">$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>
+        <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.