Mercurial > repos > saskia-hiltemann > annovar

changeset 1:7d9353127f8a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
tool_data_table_conf.xml.sample fix
author saskia-hiltemann
date Tue, 05 Nov 2013 07:16:32 -0500
parents d3a72e55deca
children 565c0e690238
files tool-data/annovar.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.sample~ tool_dependencies.xml tool_dependencies.xml~ tools/annovar/annovar.xml
diffstat 6 files changed, 33 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/tool-data/annovar.loc.sample	Wed Sep 18 10:51:20 2013 -0400
+++ b/tool-data/annovar.loc.sample	Tue Nov 05 07:16:32 2013 -0500
@@ -1,5 +1,5 @@
 #loc file for annovar tool
-
+#
 # <columns>value, dbkey, name, ANNOVAR_scripts, ANNOVAR_humandb</columns>
 
 hg18	hg18	build 36 (hg18)	/path/to/annovarscripts	/path/to/humandb
--- a/tool_data_table_conf.xml.sample	Wed Sep 18 10:51:20 2013 -0400
+++ b/tool_data_table_conf.xml.sample	Tue Nov 05 07:16:32 2013 -0500
@@ -1,5 +1,7 @@
 <!-- ANNOVAR files -->
+<tables>
 <table name="annovar_loc" comment_char="#">
 <columns>value, dbkey, name, ANNOVAR_scripts, ANNOVAR_humandb</columns>
 <file path="tool-data/annovar.loc" /> 
 </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample~	Tue Nov 05 07:16:32 2013 -0500
@@ -0,0 +1,5 @@
+<!-- ANNOVAR files -->
+<table name="annovar_loc" comment_char="#">
+<columns>value, dbkey, name, ANNOVAR_scripts, ANNOVAR_humandb</columns>
+<file path="tool-data/annovar.loc" /> 
+</table>
--- a/tool_dependencies.xml	Wed Sep 18 10:51:20 2013 -0400
+++ b/tool_dependencies.xml	Tue Nov 05 07:16:32 2013 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-	<package name="cgatools17" version="1"> 
+	<package name="cgatools" version="1.7"> 
         <install version="1.0">
             <actions>                				
                 <action type="download_by_url">http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz</action>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml~	Tue Nov 05 07:16:32 2013 -0500
@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="cgatools17" version="1"> 
+        <install version="1.0">
+            <actions>                				
+                <action type="download_by_url">http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz</action>
+				<action type="shell_command"> chmod a+x bin/cgatools</action>
+                <action type="move_file">
+                	<source>bin/cgatools</source>
+                	<destination>$INSTALL_DIR/bin</destination>
+                </action>	    
+				<action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+                </action>            	               			
+            </actions>
+        </install>
+        <readme>
+			Downloads and installs the cgatools binary. 
+        </readme>
+    </package>      
+</tool_dependency>
+
--- a/tools/annovar/annovar.xml	Wed Sep 18 10:51:20 2013 -0400
+++ b/tools/annovar/annovar.xml	Tue Nov 05 07:16:32 2013 -0500
@@ -2,7 +2,7 @@
 	<description> Annotate a file using ANNOVAR </description>
 	
 	<requirements>		
-		<requirement type="package" version="1">cgatools17</requirement>
+		<requirement type="package" version="1.7">cgatools</requirement>
 	</requirements>
 	
 	<command interpreter="bash">