# HG changeset patch
# User iuc
# Date 1391778782 18000
# Node ID 3d6beba7393ec25e2c865fcae6faf53698b8092b

Uploaded

diff -r 000000000000 -r 3d6beba7393e tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Feb 07 08:13:02 2014 -0500
@@ -0,0 +1,32 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="tabix" version="0.2.6">
+        <install version="1.0">
+            <actions>
+             <action type="download_by_url">http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>tabix</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bgzip</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="TABIX_BIN_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Installs tabix version 0.2.6. Available binaries: tabix, bgzip
+            http://samtools.sourceforge.net/tabix.shtml
+
+            Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line. 
+            The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing, 
+            tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". 
+            Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally. 
+        </readme>
+    </package>
+</tool_dependency>