# HG changeset patch
# User crs4
# Date 1385373592 18000
# Node ID 5e43533e3ed96a50d5bda16688e9833faab08c37
# Parent  d78b8fe7ca83d0aff8bf0aa088c4b3891b2a54ed
Use package_blat_35x1 in tool_dependencies.xml. Add readme.rst .

diff -r d78b8fe7ca83 -r 5e43533e3ed9 readme.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Mon Nov 25 04:59:52 2013 -0500
@@ -0,0 +1,24 @@
+BLAT wrapper
+============
+
+Install
+-------
+
+This BLAT wrapper let you install `BLAT`_ tool dependency automatically. In order to do this, you need to:
+
+- have Galaxy release_2013.11.04 or later;
+- respect BLAT licensing: BLAT source and executables are freely available for academic, nonprofit and personal use. Commercial licensing information is available on the `Kent Informatics website`_.
+
+.. _BLAT: http://genome.ucsc.edu/FAQ/FAQblat.html
+.. _Kent Informatics website: http://www.kentinformatics.com/
+
+Version history
+---------------
+
+- Release 1 (blat_wrapper 0.2): Initial release in the Tool Shed.
+- Release 2 (blat_wrapper 0.2): Add version_command element. Add test case from `Joachim Jacob's blat wrapper`_. Add readme section to tool_dependencies.xml .
+- Release 3 (blat_wrapper 0.3): Add the possibility to use locally installed FASTA or 2bit files as database source.
+- Release 4 (blat_wrapper 0.3): Depend on `package_blat_35x1`_ instead of compiling BLAT (requires Galaxy release_2013.11.04 or later).
+
+.. _Joachim Jacob's blat wrapper: http://testtoolshed.g2.bx.psu.edu/view/joachim-jacob/blat
+.. _package_blat_35x1: http://toolshed.g2.bx.psu.edu/view/iuc/package_blat_35x1
diff -r d78b8fe7ca83 -r 5e43533e3ed9 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 04 09:06:48 2013 -0500
+++ b/tool_dependencies.xml	Mon Nov 25 04:59:52 2013 -0500
@@ -1,23 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="blat" version="35">
-<!--    <repository name="package_blat_35x1" owner="iuc" /> This may be used instead of everything inside <install> when a stable Galaxy release will support the 'download_binary' action type -->
-    <install version="1.0">
-      <actions>
-        <action type="download_by_url" target_filename="blatSrc.zip">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action>
-        <action type="shell_command">export MACHTYPE=`uname -m` &amp;&amp; export HOME=$INSTALL_DIR &amp;&amp; mkdir -p $HOME/bin/$MACHTYPE &amp;&amp; make</action>
-        <action type="set_environment">
-          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/`uname -m`</environment_variable>
-        </action>
-      </actions>
-    </install>
-    <readme>
-BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html
-Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git
-
-Please note that the BLAT source and executables are freely available for
-academic, nonprofit and personal use. Commercial licensing information is
-available on the Kent Informatics website (http://www.kentinformatics.com/).
-    </readme>
+    <repository changeset_revision="84c54f1fa280" name="package_blat_35x1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
 </tool_dependency>