Mercurial > repos > matt-shirley > ncbi_sra_toolkit

changeset 7:e724bff23fb6

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Bump SRA toolkit version
author Matt Shirley <mdshw5@gmail.com>
date Thu, 13 Mar 2014 16:08:12 -0400
parents e4c21444a3ba
children 558a88cd49e4
files tool_dependencies.xml
diffstat 1 files changed, 10 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Thu Mar 13 15:30:54 2014 -0400
+++ b/tool_dependencies.xml	Thu Mar 13 16:08:12 2014 -0400
@@ -1,34 +1,34 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="sra_toolkit" version="2.3.3-3">
+  <package name="sra_toolkit" version="2.3.4-2">
     <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="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.4-2/sra_sdk-2.3.4-2.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">$INSTALL_DIR/ncbi/public</action>	
+        <action type="make_directory">$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 
+    <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 
+  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