# HG changeset patch
# User bgruening
# Date 1370500422 14400
# Node ID 6db18ec30d4c8c16971c060e1edf9142482254c5
# Parent  ac172e20bf20c0873f9bb4ac917b2d8db41a3c3f
Uploaded

diff -r ac172e20bf20 -r 6db18ec30d4c tool_dependencies.xml
--- a/tool_dependencies.xml	Mon May 27 13:31:52 2013 +0200
+++ b/tool_dependencies.xml	Thu Jun 06 02:33:42 2013 -0400
@@ -1,64 +1,18 @@
+<?xml version="1.0"?>
 <tool_dependency>
-    <package name="openbabel" version="2.3.2">
-        <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-    </package>
-    <package name="graphicsmagick" version="1.3.18">
-        <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-    </package>
-    <package name="osra" version="2.0.0">
+    <package name="fastqc_dist_0_10_1" version="0.10.1">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz</action>
-
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="openbabel" version="2.3.2" />
-                    </repository>
-                    <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="graphicsmagick" version="1.3.18" />
-                    </repository>
-                </action>
-                <action type="shell_command">wget http://potrace.sourceforge.net/download/potrace-1.11.tar.gz</action>
-                <action type="shell_command">tar xfvz potrace-1.11.tar.gz &amp;&amp; cd potrace-1.11 &amp;&amp; ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build &amp;&amp; make &amp;&amp; make install</action>
-
-                <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action>
-                <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz &amp;&amp; cd gocr-0.50pre-patched &amp;&amp; ./configure --prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; make all install</action>
-
-
-                
-                <action type="shell_command">wget http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz</action>
-                <action type="shell_command">tar xfvz tclap-1.2.1.tar.gz &amp;&amp; cd tclap-1.2.1 &amp;&amp; ./configure --prefix=$INSTALL_DIR/tclap/build &amp;&amp; make &amp;&amp; make install</action>
-
-                
-                <action type="shell_command">wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action>
-                <action type="shell_command">tar xfvz ocrad-0.21.tar.gz &amp;&amp; cd ocrad-0.21 &amp;&amp; ./configure --prefix=$INSTALL_DIR/ocrad/build &amp;&amp; make &amp;&amp; make install</action>
-
-                
-                <action type="shell_command">wget https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2</action>
-                <action type="shell_command">tar xfvj cuneiform-linux-1.1.0.tar.bz2 &amp;&amp; cd cuneiform-linux-1.1.0 &amp;&amp; mkdir build &amp;&amp; cd build &amp;&amp; cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ &amp;&amp; make &amp;&amp; make install</action>
-
-                
-                
-                <action type="shell_command">export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/bin/ &amp;&amp; 
-                    ./configure --with-tclap-include=$INSTALL_DIR/tclap/build/include/ --with-potrace-include=$INSTALL_DIR/potrace/build/include/ --with-potrace-lib=$INSTALL_DIR/potrace/build/lib/ --with-gocr-include=$INSTALL_DIR/gocr/build/include/gocr/ --with-gocr-lib=$INSTALL_DIR/gocr/build/lib/ --with-ocrad-include=$INSTALL_DIR/ocrad/build/include/ --with-ocrad-lib=$INSTALL_DIR/ocrad/build/lib/ --with-cuneiform-include=$INSTALL_DIR/cuneiform/build/install/include/ --with-cuneiform --with-cuneiform-lib=$INSTALL_DIR/cuneiform/build/install/lib/ --with-openbabel-include=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ --with-openbabel-lib=$OPENBABEL_LIB_DIR --with-graphicsmagick-lib=$GRAPHICSMAGICK_ROOT_DIR/lib/ --with-graphicsmagick-include=$GRAPHICSMAGICK_ROOT_DIR/include/GraphicsMagick/ --prefix=$INSTALL_DIR </action>
-                <action type="shell_command">make</action>
-                <action type="shell_command">make install</action>
-
-                <action type="shell_command">rm $INSTALL_DIR/tclap/ -r</action>
-                
-                <action type="shell_command">rm $INSTALL_DIR/gocr/ -r</action>
-                <action type="shell_command">rm $INSTALL_DIR/ocrad/ -r</action>
-                <action type="shell_command">rm $INSTALL_DIR/cuneiform/ -r</action>
-
+                <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action>
+                <action type="move_directory_files">
+                    <source_directory>../FastQC</source_directory>
+                    <destination_directory>$INSTALL_DIR/fastqc_dist</destination_directory>
+                </action>                
+                <action type="shell_command">chmod ugo+x $INSTALL_DIR/fastqc_dist/fastqc</action>
                 <action type="set_environment">
-                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$GRAPHICSMAGICK_ROOT_DIR/lib/</environment_variable>
-                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    
-                    <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/fastqc_dist</environment_variable>
                 </action>
             </actions>
         </install>
-        <readme>We still have a handfull of requirements</readme>
     </package>
 </tool_dependency>