Mercurial > repos > crs4 > edge_pro

diff tool_dependencies.xml @ 3:ddcbf8732706 draft

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Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
author crs4
date Mon, 19 Jan 2015 12:48:51 -0500
parents f77ce4f92b46
children
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--- a/tool_dependencies.xml	Wed Mar 05 06:44:35 2014 -0500
+++ b/tool_dependencies.xml	Mon Jan 19 12:48:51 2015 -0500
@@ -1,12 +1,14 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="bowtie2" version="2.1.0">
-    <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="edge-pro" version="1.3.1">
     <install version="1.0">
       <actions>
         <action type="download_by_url">http://ccb.jhu.edu/software/EDGE-pro/EDGE_pro_v1.3.1.tar.gz</action>
+        <!-- Search executables in PATH instead of the CWD -->
+        <action type="shell_command">sed -i -e 's|$sourceDir/||' edge.pl</action>
         <action type="shell_command">make</action>
         <action type="move_file">
           <source>count</source>