# HG changeset patch
# User s-kaufmann
# Date 1408106152 14400
# Node ID a6c5e5a410252ca1cd26fa3e04a4ebe3836c82da
# Parent  dd2fdd397831caf6184293e9956c204108d510c2
Uploaded

diff -r dd2fdd397831 -r a6c5e5a41025 circos.conf
--- a/circos.conf	Wed Jul 30 08:23:49 2014 -0400
+++ b/circos.conf	Fri Aug 15 08:35:52 2014 -0400
@@ -1,7 +1,7 @@
 <image>
 png = yes
-dir = /home/steffi/Software/galaxy-dist/database/job_working_directory/000/105/dataset_164_files
-file = /home/steffi/Software/galaxy-dist/database/files/000/dataset_164.dat.png
+dir = /home/steffi/Software/galaxy-dist/database/job_working_directory/000/117/dataset_187_files
+file = /home/steffi/Software/galaxy-dist/database/files/000/dataset_187.dat.png
 radius = 750p
 background=white
 image_map_use = yes
@@ -10,18 +10,18 @@
 auto_alpha_colors = yes
 auto_alpha_steps  = 5
 </image>
-karyotype = /home/steffi/Software/galaxy-dist/database/files/000/dataset_162.dat.karyotype
+karyotype = /home/steffi/Software/galaxy-dist/database/files/000/dataset_185.dat.karyotype
 chromosomes_units = 1000000
 chromosomes_display_default = no
 <colors>
-<<include /home/steffi/Software/shed_tools/toolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper/67eb55a9debe/synteny_mapper/circos-files/colors.synteny.conf>>
-<<include /home/steffi/Software/shed_tools/toolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper/67eb55a9debe/synteny_mapper/circos-files/colors.mouse.conf>>
+<<include /home/steffi/Software/shed_tools/toolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper/5d6d452a8e0b/synteny_mapper/circos-files/colors.synteny.conf>>
+<<include /home/steffi/Software/shed_tools/toolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper/5d6d452a8e0b/synteny_mapper/circos-files/colors.mouse.conf>>
 </colors>
 chromosomes = hs44454;mm44454
 <highlights>
 z = 5
 <highlight>
-file = /home/steffi/Software/galaxy-dist/database/files/000/dataset_161.dat.gene-track
+file = /home/steffi/Software/galaxy-dist/database/files/000/dataset_186.dat.gene-track
 r0 = 0.9r
 r1 = 0.99r
 stroke_thickness = 1
@@ -32,7 +32,7 @@
 <plot>
 type=text
 color=black
-file=/home/steffi/Software/galaxy-dist/database/files/000/dataset_161.dat.gene-track-labels
+file=/home/steffi/Software/galaxy-dist/database/files/000/dataset_186.dat.gene-track-labels
 r0=0.99r
 r1=1.5r
 label_size=9
@@ -48,7 +48,7 @@
 </plots>
 <links>
 <link>
-file = /home/steffi/Software/galaxy-dist/database/files/000/dataset_161.dat.links
+file = /home/steffi/Software/galaxy-dist/database/files/000/dataset_186.dat.links
 radius = 0.88r
 bezier_radius = 0r
 color = link_a4
@@ -78,7 +78,7 @@
 </rules>
 </link>
 <link>
-file = /home/steffi/Software/galaxy-dist/database/files/000/dataset_161.dat.jumped
+file = /home/steffi/Software/galaxy-dist/database/files/000/dataset_186.dat.jumped
 radius = 0.88r
 bezier_radius = 0r
 color = link_jumped_a4
@@ -108,4 +108,4 @@
 </rules>
 </link>
 </links>
-<<include /home/steffi/Software/shed_tools/toolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper/67eb55a9debe/synteny_mapper/circos-files/synteny-region-default.conf>>
+<<include /home/steffi/Software/shed_tools/toolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper/5d6d452a8e0b/synteny_mapper/circos-files/synteny-region-default.conf>>
diff -r dd2fdd397831 -r a6c5e5a41025 syntenyMapper.jar
Binary file syntenyMapper.jar has changed
diff -r dd2fdd397831 -r a6c5e5a41025 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jul 30 08:23:49 2014 -0400
+++ b/tool_dependencies.xml	Fri Aug 15 08:35:52 2014 -0400
@@ -25,6 +25,34 @@
         <readme>
 Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed.
         </readme>
-    </package>      
+    </package>  
+
+ <package name="R_3_0_1" version="3.0.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action>
+                <!--<action type="set_environment_for_install">
+                    <repository name="package_readline_6_2" owner="iuc">
+                        <package name="readline" version="6.2" />
+                    </repository>
+                </action>-->
+
+                <action type="shell_command">
+                    ./configure --with-readline=no --enable-R-shlib  --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR/bin/ --datarootdir=$INSTALL_DIR/share/
+                </action>
+                <action type="shell_command">make</action>
+                <action type="shell_command">make install</action>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
+                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
+                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
+                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
+                    <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
+    </package>    
 
 </tool_dependency>
diff -r dd2fdd397831 -r a6c5e5a41025 visualization.xml
--- a/visualization.xml	Wed Jul 30 08:23:49 2014 -0400
+++ b/visualization.xml	Fri Aug 15 08:35:52 2014 -0400
@@ -5,10 +5,12 @@
     <requirement type="set_environment">JAR_PATH</requirement>
     <requirement type="package" version="0.64">circos</requirement>
     <requirement type="set_environment">CIRCOS_SCRIPT_PATH</requirement>
+    <requirement type="package" version="3.0.1">R_3_0_1</requirement>
+    <requirement type="set_environment">R_PATH</requirement>
 </requirements>
 
   <command>
-	java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/visualization/SyntenyPlotterWrapper $syntenyRegion $mappingFile $syntenyFile $out_file1 \$CIRCOS_PATH \$CIRCOS_SCRIPT_PATH $out_file1.files_path
+	java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/visualization/SyntenyPlotterWrapper $syntenyRegion $mappingFile $syntenyFile $out_file1 \$CIRCOS_PATH \$CIRCOS_SCRIPT_PATH $out_file1.files_path $linear \$R_PATH
   </command>
 
 <inputs>
@@ -23,6 +25,10 @@
 			<filter type="sort_by" column="0" ref="syntenyFile"/>
 		</options>
 	</param>
+	<param name="linear" type="select" label="Linear">
+			<option value="false">Circular representation</option>
+			<option value="true">Linear representation</option>
+	</param>
 </inputs>
   <outputs>
     <data format="html" name="out_file1" label="Visualization of Mapping"/>