Mercurial > repos > nikos > bigwig_to_wig

changeset 2:bce77c02cc5f draft

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Fixed tool dependency errors
author nikos
date Tue, 05 Aug 2014 09:03:05 -0400
parents 561c9a746a81
children f15581b3424e
files bigwig_to_wig.xml tool_dependencies.xml
diffstat 2 files changed, 21 insertions(+), 27 deletions(-) [+]
line wrap: on
line diff
--- a/bigwig_to_wig.xml	Tue Aug 05 07:51:14 2014 -0400
+++ b/bigwig_to_wig.xml	Tue Aug 05 09:03:05 2014 -0400
@@ -1,9 +1,9 @@
 <tool id="bigwig_to_wig" name="BigWig to Wig" version="1.0.2">
     <description>converter</description>
-    <command>bigwig_to_wig.sh -f $input -b $bin_size -l $mylab > $output </command>
+    <command interpreter="bash">bigwig_to_wig.sh -f $input -b $bin_size -l $mylab > $output </command>
   <requirements>
-      <requirement type="package">bigWigSummary</requirement>
-      <requirement type="package">bigWigInfo</requirement>
+      <requirement type="package" version="1.0">bigWigSummary</requirement>
+      <requirement type="package" version="1.0">bigWigInfo</requirement>
   </requirements>
   <inputs>
       <param format="bigwig" name="input" type="data" label="BigWig file to convert" />
--- a/tool_dependencies.xml	Tue Aug 05 07:51:14 2014 -0400
+++ b/tool_dependencies.xml	Tue Aug 05 09:03:05 2014 -0400
@@ -1,41 +1,35 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="bigWigSummary">
+    <package name="bigWigSummary" version="1.0">
         <install version="1.0">
-	    <actions_group>
-                <actions os="linux" architecture="x86_64">
-                    <action type="download_binary"><url_template>http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary</url_template></action>
-	            <action type="move_directory_files">
-            		<source_directory>.</source_directory>
-            		<destination_directory>$INSTALL_DIR</destination_directory>
-        	    </action>
-		</actions>
-
-
+            <actions>
+                <action type="download_by_url">http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary</action>
+	        <action type="move_directory_files">
+        	    <source_directory>.</source_directory>
+        	    <destination_directory>$INSTALL_DIR</destination_directory>
+        	</action>
+                <action type="chmod"><file mode="755">$INSTALL_DIR/bigWigSummary</file></action>
 		<action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                 </action>
-            </actions_group>
+	    </actions>
         </install>
         <readme>
         </readme>
     </package>
-    <package name="bigWigInfo">
+    <package name="bigWigInfo" version="1.0">
         <install version="1.0">
-            <actions_group>
-                <actions os="linux" architecture="x86_64">
-                    <action type="download_binary"><url_template>http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template></action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-
-
+            <actions>
+                <action type="download_by_url">http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+		<action type="chmod"><file mode="755">$INSTALL_DIR/bigWigInfo</file></action>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                 </action>
-            </actions_group>
+            </actions>
         </install>
         <readme>
         </readme>