diff tool_dependencies.xml @ 2:bc4451edb703 draft

Update Orione citation. Update dependency to SSPACE Basic v2.1 . Add <citations>.

--- a/tool_dependencies.xml	Fri Feb 21 04:17:55 2014 -0500
+++ b/tool_dependencies.xml	Mon Oct 27 14:11:57 2014 -0400
@@ -1,17 +1,18 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="sspace" version="2.0">
+  <package name="bowtie" version="1.0.0">
+    <repository changeset_revision="9fcaaedbbfd6" name="package_bowtie_1_0_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="sspace" version="2.1">
     <install version="1.0">
       <actions>
-        <action type="download_by_url" target_filename="SSPACE-BASIC-2.0_linux-x86_64.zip">http://www.baseclear.com/download.php?file_id=1038</action>
-        <!-- fix for Perl >= 5.16.0-->
-        <action type="shell_command">sed -i -e 's/require "getopts.pl"/use Getopt::Std/' -e 's/&amp;Getopts/getopts/' SSPACE_Basic_v2.0.pl</action>
+        <action target_filename="sspace_basic-2.1.tar.gz" type="download_by_url">https://github.com/nsoranzo/sspace_basic/archive/v2.1.tar.gz</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
           <destination_directory>$INSTALL_DIR</destination_directory>
         </action>
         <action type="set_environment">
-          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
         </action>
       </actions>
     </install>