Mercurial > repos > iuc > bedtools

changeset 3:190a747ddaa8 draft

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Uploaded
author bgruening
date Sat, 03 Jan 2015 16:23:23 -0500
parents effb7b4e45ed
children 315929597efb
files tool_dependencies.xml
diffstat 1 files changed, 12 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Dec 05 13:31:24 2014 -0500
+++ b/tool_dependencies.xml	Sat Jan 03 16:23:23 2015 -0500
@@ -1,20 +1,22 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="weka" version="3.6.11">
+    <package name="bedtools" version="2.22">
         <install version="1.0">
-            <actions> 
-                <action type="download_by_url">http://sourceforge.net/projects/weka/files/weka-3-6/3.6.11/weka-3-6-11.zip</action>
-                <action type="move_file">
-                    <source>weka-3-6-11/weka.jar</source>
-                    <destination>$INSTALL_DIR</destination>
+            <actions>
+                <action type="download_by_url">https://github.com/arq5x/bedtools2/releases/download/v2.22.1/bedtools-2.22.1.tar.gz</action>
+                <action type="shell_command">make</action>
+                <action type="move_directory_files">
+                    <source_directory>bin</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
                 </action>
                 <action type="set_environment">
-                    <environment_variable name="WEKA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions>
         </install>
-        <readme>
-            Weka requires a JAVA (1.5+) runtime evironment.
-        </readme>
+        <readme>BEDTools is a collection of utilities for comparing, summarizing, and intersecting genomic features in BED, GTF/GFF, VCF and BAM formats.</readme>
     </package>
 </tool_dependency>
+
+
+