# HG changeset patch
# User iuc
# Date 1392745946 18000
# Node ID cc0f4b49b6f1da664102c9f32131742fbd04b5fd
# Parent  b355179ea459f817526f43b1c7250af6dfb65fae
Uploaded

diff -r b355179ea459 -r cc0f4b49b6f1 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jan 29 16:13:18 2014 -0500
+++ b/tool_dependencies.xml	Tue Feb 18 12:52:26 2014 -0500
@@ -1,36 +1,28 @@
+<?xml version="1.0"?>
 <tool_dependency>
+    <package name="libpng" version="1.6.7">
+        <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
     <package name="blat" version="35x1">
         <install version="1.0">
             <actions>
-
-                <action type="download_binary">
-                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</url_template>
-                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/blat/blat</url_template>
-                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/blat/blat</url_template>
-                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blat/blat</url_template>
-                </action>
-
-                <action type="move_file">
-                    <source>$INSTALL_DIR/blat</source>
-                    <destination>$INSTALL_DIR/blat</destination>
-                </action>
-                <action type="chmod">
-                    <file mode="755">$INSTALL_DIR/blat</file>
+                <!-- finally go back to the original version and compile blat and the entire server from source 
+                    Thanks to Nicola Soranzo.
+                    The problem is that the binaries are not versioned and we can't guarantee reproducibility. 
+                    The only way to download the source code of minor releases is from the git repository.
+                -->
+                <action type="shell_command">git clone git://genome-source.cse.ucsc.edu/kent.git blat</action>
+                <action type="shell_command">git reset --hard 84614918e462d7750a8f56e5ce9540c623b87b48</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="libpng" version="1.6.7" />
+                    </repository>
                 </action>
+                <action type="shell_command">export HOME=$INSTALL_DIR &amp;&amp; export MACHTYPE=`uname -m` &amp;&amp; export PNGINCL=-I${LIBPNG_ROOT}/include &amp;&amp; export PNGLIB="-L${LIBPNG_ROOT}/lib -lpng" &amp;&amp; mkdir -p $HOME/bin/$MACHTYPE &amp;&amp; make -C src/lib/ &amp;&amp; make -C src/jkOwnLib/ &amp;&amp; make -C src/blat/ &amp;&amp; mv $INSTALL_DIR/bin/$MACHTYPE/* $INSTALL_DIR/bin/ &amp;&amp; rm -rf $INSTALL_DIR/.ccache/</action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="append_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="BLAT_PATH" action="append_to">$INSTALL_DIR</environment_variable>
+                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
+                  <environment_variable action="set_to" name="BLAT_PATH">$INSTALL_DIR</environment_variable>
                 </action>
-
-                <!--
-                Alternative version from Nicola Soranzo.
-                <action type="download_by_url" target_filename="blatSrc.zip">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action>
-                <action type="shell_command">export MACHTYPE=`uname -m` &amp;&amp; export HOME=$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>