# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1370464677 18000
# Node ID 06675bd664eeba028a8fe3a489cbc690303b815f
# Parent  f4eadbd2e7c1e217b3324986686c08838e15af09
Update to DeFuse verion 0.6.1 and change tool dependencies for autoinstall

diff -r f4eadbd2e7c1 -r 06675bd664ee README
--- a/README	Fri Jan 18 14:56:40 2013 -0600
+++ b/README	Wed Jun 05 15:37:57 2013 -0500
@@ -1,4 +1,4 @@
-The DeFuse galaxy tool is based on DeFuse_Version_0.6.0
+The DeFuse galaxy tool is based on DeFuse_Version_0.6.1
 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
 
 DeFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion.
@@ -35,7 +35,9 @@
 These datasets should be referenced in the tool-data/defuse.loc file. 
 
 
-External Tools  ( http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.0 )
+Galaxy will try to auto-install dependencies:
+
+External Tools  ( http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1 )
 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 samtools
 The latest version of samtools can be downloaded from sourceforge: https://sourceforge.net/projects/samtools/files/samtools.
diff -r f4eadbd2e7c1 -r 06675bd664ee defuse.xml
--- a/defuse.xml	Fri Jan 18 14:56:40 2013 -0600
+++ b/defuse.xml	Wed Jun 05 15:37:57 2013 -0500
@@ -1,12 +1,11 @@
-<tool id="defuse" name="DeFuse" version="1.6">
+<tool id="defuse" name="DeFuse" version="1.6.1">
  <description>identify fusion transcripts</description>
  <requirements>
-  <requirement type="package" version="0.6.0">defuse</requirement>
+  <requirement type="package" version="0.6.1">defuse</requirement>
   <requirement type="package" version="0.1.18">samtools</requirement>
-  <requirement type="package" version="0.12.7">bowtie</requirement>
-  <requirement type="package" version="2012-07-20">gmap</requirement>
-  <requirement type="package" version="34x10">blat</requirement>
-  <requirement type="package" version="34x10">fatotwobit</requirement>
+  <requirement type="package" version="1.0.0">bowtie</requirement>
+  <requirement type="package" version="2013-05-09">gmap</requirement>
+  <requirement type="package" version="283">kent</requirement>
  </requirements>
   <command interpreter="command"> /bin/bash $shscript </command>
  <inputs>
diff -r f4eadbd2e7c1 -r 06675bd664ee repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Wed Jun 05 15:37:57 2013 -0500
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<repositories description="External software packages used by DeFuse">
+    <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="03bb09b717ae" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="d4c8accb9a57" name="package_kent_283" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+</repositories>
diff -r f4eadbd2e7c1 -r 06675bd664ee tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jan 18 14:56:40 2013 -0600
+++ b/tool_dependencies.xml	Wed Jun 05 15:37:57 2013 -0500
@@ -1,10 +1,31 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="defuse" version="0.6.0">
+    <package name="boost" version="1.53.0">
+        <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" prior_installation_required="True" toolshed="http://localhost:19009" />
+    </package>
+    <package name="samtools" version="0.1.18">
+        <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bowtie" version="1.0.0">
+        <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="gmap" version="2013-05-09">
+        <repository changeset_revision="03bb09b717ae" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="kent" version="283">
+        <repository changeset_revision="d4c8accb9a57" name="package_kent_283" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="defuse" version="0.6.1">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.0.tar.gz</action>
-                <action type="shell_command">cd tools &amp;&amp; make</action>
+                <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.1.tar.gz</action>
+                <!-- populate the environment variables from the dependent repos -->
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" prior_installation_required="True" toolshed="http://localhost:19009" >
+                        <package name="boost" version="1.53.0" />
+                    </repository>
+                </action>
+                <action type="shell_command">export CPLUS_INCLUDE_PATH=$BOOST_ROOT_DIR:$CPLUS_INCLUDE_PATH &amp;&amp; cd tools &amp;&amp; make</action>
                 <action type="move_directory_files">
                     <source_directory>.</source_directory>
                     <destination_directory>$INSTALL_DIR</destination_directory>
@@ -20,161 +41,4 @@
         </readme>
     </package>
 
-    <package name="samtools" version="0.1.18">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
-                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>samtools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>misc/maq2sam-long</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-Compiling SAMtools requires the ncurses and zlib development libraries.
-        </readme>
-    </package>
-
-
-    <package name="bowtie" version="0.12.7">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>bowtie</source>
-                    <destination>$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">$INSTALL_DIR/bin</environment_variable>
-            </action>
-            </actions>
-        </install>
-        <readme>
-            Compiling Bowtie requires libpthread to be present on your system.
-        </readme>
-    </package>
-
-    <package name="gmap" version="2012-07-20">
-        <install version="1.0">
-            <actions>
-	        <action type="download_by_url" target_filename="gmap-2012-07-20.tar.gz">http://research-pub.gene.com/gmap/src/gmap-gsnap-2012-07-20.v2.tar.gz</action>
-                <action type="shell_command">./configure</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>src/gmap</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>src/gmapindex</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>src/gsnap</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>src/uniqscan</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>src/iit_store</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>src/iit_get</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>src/atoiindex</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>src/snpindex</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>src/cmetindex</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>src/get-genome</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_directory_files">
-                    <source_directory>util</source_directory>
-                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-
-    <package name="blat" version="34x10">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
-                <action type="shell_command">chmod 755 blat</action>
-                <action type="move_file">
-                    <source>blat</source>
-                    <destination>$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>