# HG changeset patch
# User geert-vandeweyer
# Date 1392982715 18000
# Node ID 6ddc1c6472ef47152a9c604ba9f974de60b535dd
# Parent  7ebc71784e9f8699162f0686eaeaff68e9b918f2
Macro corrections

diff -r 7ebc71784e9f -r 6ddc1c6472ef VCF_to_VariantDB.pl
--- a/VCF_to_VariantDB.pl	Wed Feb 19 06:53:47 2014 -0500
+++ b/VCF_to_VariantDB.pl	Fri Feb 21 06:38:35 2014 -0500
@@ -81,6 +81,8 @@
 	die("ERROR: $content");
 }
 
+print $opts{'H'}. " was specified as galaxy host\n";
+
 ###############################################
 ## SEND THE VCF AND BAM FILES FOR PROCESSING ##
 ###############################################
diff -r 7ebc71784e9f -r 6ddc1c6472ef VCF_to_VariantDB_macros.xml
--- a/VCF_to_VariantDB_macros.xml	Wed Feb 19 06:53:47 2014 -0500
+++ b/VCF_to_VariantDB_macros.xml	Fri Feb 21 06:38:35 2014 -0500
@@ -6,6 +6,6 @@
     </requirements>
   </xml>
   <token name="@URL@">
-    "\$GALAXY_URL/"
+    $GALAXY_URL/
   </token>
 </macros>
diff -r 7ebc71784e9f -r 6ddc1c6472ef readme.rst
--- a/readme.rst	Wed Feb 19 06:53:47 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-Galaxy wrapper for VariantDB Import
-===================================
-
-This wrapper and VariantDB is written by Geert Vandeweyer. 
-
-The recommended installation is by means of the toolshed_.
-
-.. _toolshed: http://toolshed.g2.bx.psu.edu/view/geert-vandeweyer/vcf_to_variantdb
-
-Galaxy should be able to install the needed perl module dependencies automatically
-for you. To allow your server to communicate with VariantDB, you must edit the GALAXY_URL environment variable in the file:
-
-<tool_dependency_dir>/environment_settings/GALAXY_URL/geert-vandeweyer/vcf_to_variantdb/<hash_string>/env.sh
-
-to point to the full URL of the server (e.g: http://biominavm-galaxy.biomina.be/galaxy ) where you have installed the wrapper.
-
-Finally, if you also have a private VariantDB instance, you need to add it to the wrapper configuration file, as an extra option.
diff -r 7ebc71784e9f -r 6ddc1c6472ef tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Feb 19 06:53:47 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="GALAXY_URL">http://your.galaxy.server/and_sub_path/</environment_variable>
-    </set_environment>
-    <package name="perl_module_libwww" version="6.05">
-        <repository changeset_revision="f217bf3faf3b" name="package_perl_libwww" owner="geert-vandeweyer" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>