# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1357333279 21600
# Node ID 3bd1087db05e53c560b3614c4c8bbfec42bcdc11
# Parent  679a5c7b12943158f9f4e6b008f47b9823f9be41
Add dependecies for bowtie, blat, and faToTwoBit

diff -r 679a5c7b1294 -r 3bd1087db05e README
--- a/README	Fri Jan 04 13:29:03 2013 -0600
+++ b/README	Fri Jan 04 15:01:19 2013 -0600
@@ -9,6 +9,7 @@
 
 The included tool_dependencies.xml will download and install the defuse code.  
 It will set the environment variable: "DEFUSE_PATH" to the location of the defuse install.  
+The tool_dependencies.xml also has the download for bowtie.
 
 
 The defuse.pl command relies on a configuration file to specifiy options, the location of reference data, and other applications that it depends upon: bowtie, bowtie-build, samtools, blat, fatotwobit, R, and Rscript.
@@ -32,4 +33,19 @@
 These datasets should be referenced in the tool-data/defuse.loc file. 
 
 
+External Tools
+deFuse relies on other publically available tools as part of its pipeline. Some of these tools are not included with the deFuse download. Obtain these tools as detailed below.
+Download bowtie: 
+The latest version of bowtie can be downloaded from sourceforge: http://sourceforge.net/projects/bowtie-bio/files/bowtie/. deFuse has been tested on version 0.12.5.
+Set the bowtie_bin and bowtie_build_bin entries in config.txt to the fully qualified paths of the bowtie and bowtie-build binaries.
+Download blat and faToTwoBit
+The latest blat tool suite can be downloaded from the ucsc website: http://hgdownload.cse.ucsc.edu/admin/exe/. Download blat and faToTwoBit and set the blat_bin and fatotwobit_bin entries in config.txt to the fully qualified paths of the blat and faToTwoBit binaries.
+Download R
+The latest version of R can be downloaded from the R project website: http://www.r-project.org/. Install R and then locate the R and Rscript executables, and set the r_bin and rscript_bin entries in config.txt to the path of those executables.
+Install the kernlab package. Run R, then at the prompt type install.packages("kernlab")
+Creating required derivative files
+Once the required files and tools have been downloaded, the create_reference_dataset.pl script will build any derivative files including bowtie indices and 2bit files. Run the following command. Expect this step to take at least 12 hours.
+create_reference_dataset.pl -c config.txt
 
+
+
diff -r 679a5c7b1294 -r 3bd1087db05e defuse.xml
--- a/defuse.xml	Fri Jan 04 13:29:03 2013 -0600
+++ b/defuse.xml	Fri Jan 04 15:01:19 2013 -0600
@@ -2,9 +2,9 @@
  <description>identify fusion transcripts</description>
  <requirements>
   <requirement type="package" version="0.5.0">defuse</requirement>
-  <requirement type="package">bowtie</requirement>
-  <requirement type="package">blat</requirement>
-  <requirement type="package">fatotwobit</requirement>
+  <requirement type="package" version="0.12.7">bowtie</requirement>
+  <requirement type="package" version="34x10">blat</requirement>
+  <requirement type="package" version="34x10">fatotwobit</requirement>
  </requirements>
   <command interpreter="command"> /bin/bash $shscript </command>
  <inputs>
diff -r 679a5c7b1294 -r 3bd1087db05e tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jan 04 13:29:03 2013 -0600
+++ b/tool_dependencies.xml	Fri Jan 04 15:01:19 2013 -0600
@@ -18,4 +18,77 @@
         </readme>
     </package>
 
+    <package name="bowtie" version="0.12.7">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>bowtie</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bowtie-build</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bowtie-inspect</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+            </action>
+            </actions>
+        </install>
+        <readme>
+            Compiling Bowtie requires libpthread to be present on your system.
+        </readme>
+    </package>
+
+    <package name="blat" version="34x10">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
+                <action type="shell_command">chmod 755 blat</action>
+                <action type="move_file">
+                    <source>blat</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+This only handles blat for a non-commercial linux system.
+
+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>
+    </package>
+
+    <package name="fatotwobit" version="34x10">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action>
+                <action type="shell_command">chmod 755 faToTwoBit</action>
+                <action type="move_file">
+                    <source>faToTwoBit</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+This only handles faToTwoBit for a non-commercial linux system.
+
+Please note that the 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>