# HG changeset patch
# User jjohnson
# Date 1383923454 18000
# Node ID 455a4bd49c526ab255707f6a32eedb97437924c8

Uploaded

diff -r 000000000000 -r 455a4bd49c52 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Nov 08 10:10:54 2013 -0500
@@ -0,0 +1,63 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="blat_server" version="latest">
+        <install version="1.0">
+            <actions_group>
+
+                <actions os="linux" architecture="x86_64">
+                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
+                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfServer</action>
+                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfClient</action>
+                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action>
+                    <action type="shell_command">chmod ugo+x *</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+
+                <actions os="darwin" architecture="x86_64">
+                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blat</action>
+                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gfClient</action>
+                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/gfServer</action>
+                    <action type="download_file">ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/faToTwoBit</action>
+                    <action type="shell_command">chmod ugo+x *</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>
+                </actions>
+
+            <actions>
+                <action type="download_by_url" target_filename="kent.zip">http://hgdownload.cse.ucsc.edu/admin/jksrc.zip</action>
+                <action type="shell_command">
+                    export MACHTYPE=`uname -m`; 
+                    export BINDIR=$INSTALL_DIR/bin; mkdir $INSTALL_DIR/bin; 
+                    cd src/lib; make; 
+                    cd ../jkOwnLib; make; 
+                    cd ../blat; make;
+                    cd ../gfClient; make;
+                    cd ../gfServer; make;
+                    cd ../utils; mv makefile makefile.orig; grep -v -E 'pslLiftSubrangeBlat|raSqlQuery|scaffoldFaToAgp' makefile.orig > makefile;  make
+                </action>
+            </actions>
+            <action type="set_environment">
+                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+Downloads and installs the latest kent blat server tools (blat, gfServer, gfClient, faToTwoBit).
+It will try to install executable files from:  UCSC ftp://hgdownload.cse.ucsc.edu/admin/exe/
+otherwise it will try to compile from source from:  UCSC at: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
+( The website doesn't offer previously released versions. )
+
+NOTE: A license is required for use in a COMMERCIAL system.
+
+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>
+    </package>
+
+</tool_dependency>