Mercurial > repos > yhoogstrate > edger_with_design_matrix

changeset 72:e75afef75c13 draft

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Uploaded
author yhoogstrate
date Tue, 30 Sep 2014 11:24:28 -0400
parents 46896caca6be
children d72e4bf6ccae
files edgeR_Differential_Gene_Expression.xml
diffstat 1 files changed, 10 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/edgeR_Differential_Gene_Expression.xml	Tue Sep 30 11:24:21 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Tue Sep 30 11:24:28 2014 -0400
@@ -7,6 +7,9 @@
 		<!--<requirement type="package" version="3.1.0">R</requirement>-->
 		<requirement type="package" version="3.0.3">R</requirement>
 		<requirement type="package" version="latest">package_biocLite_edgeR_limma</requirement>
+		<requirement type="package" version="1.3.18">graphicsmagick</requirement>
+	</package>
+	-->
 	</requirements>
 	
 	<command>
@@ -91,42 +94,42 @@
 				#if $output_MDSplot:
 					#set $output_MDSplot_tmp = str($output_MDSplot)+".png"
 					
-					convert $output_MDSplot $output_MDSplot_tmp ; 
+					gm convert $output_MDSplot $output_MDSplot_tmp ; 
 					mv $output_MDSplot_tmp $output_MDSplot ; 
 				#end if
 				
 				#if $output_BCVplot:
 					#set $output_BCVplot_tmp = str($output_BCVplot)+".png"
 					
-					convert $output_BCVplot $output_BCVplot_tmp ; 
+					gm convert $output_BCVplot $output_BCVplot_tmp ; 
 					mv $output_BCVplot_tmp $output_BCVplot ; 
 				#end if
 				
 				#if $output_MAplot:
 					#set $output_MAplot_tmp = str($output_MAplot)+".png"
 					
-					convert $output_MAplot $output_MAplot_tmp ; 
+					gm convert $output_MAplot $output_MAplot_tmp ; 
 					mv $output_MAplot_tmp $output_MAplot ; 
 				#end if
 				
 				#if $output_PValue_distribution_plot:
 					#set $output_PValue_distribution_plot_tmp = str($output_PValue_distribution_plot)+".png"
 					
-					convert $output_PValue_distribution_plot $output_PValue_distribution_plot_tmp ; 
+					gm convert $output_PValue_distribution_plot $output_PValue_distribution_plot_tmp ; 
 					mv $output_PValue_distribution_plot_tmp $output_PValue_distribution_plot ; 
 				#end if
 				
 				#if $output_hierarchical_clustering_plot:
 					#set $output_hierarchical_clustering_plot_tmp = str($output_hierarchical_clustering_plot)+".png"
 					
-					convert $output_hierarchical_clustering_plot $output_hierarchical_clustering_plot_tmp ;  
+					gm convert $output_hierarchical_clustering_plot $output_hierarchical_clustering_plot_tmp ;  
 					mv $output_hierarchical_clustering_plot_tmp $output_hierarchical_clustering_plot ; 
 				#end if
 				
 				#if $output_heatmap_plot:
 					#set $output_heatmap_plot_tmp = str($output_heatmap_plot)+".png"
 					
-					convert $output_heatmap_plot $output_heatmap_plot_tmp ; 
+					gm convert $output_heatmap_plot $output_heatmap_plot_tmp ; 
 					mv $output_heatmap_plot_tmp $output_heatmap_plot ; 
 				#end if
 			#end if
@@ -143,7 +146,7 @@
 			grep -v 'Setting LC_COLLATE failed' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
 			
 			cat stderr.txt >&amp;2
-	
+			
 	</command>
 	
 	<inputs>