# HG changeset patch
# User yhoogstrate
# Date 1441113307 14400
# Node ID ec951a5017f8dfa1f71bc09559396280aca6ddff
# Parent  a4a4c88783eaa2a019d36066fd5411320e2ac2c8
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit a6cf3ec153ca4a3846258a223d287ca125eea7be

diff -r a4a4c88783ea -r ec951a5017f8 edgeR_Concatenate_Expression_Matrices.xml
--- a/edgeR_Concatenate_Expression_Matrices.xml	Tue Sep 01 04:59:05 2015 -0400
+++ b/edgeR_Concatenate_Expression_Matrices.xml	Tue Sep 01 09:15:07 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="concatenate_expression_matrices" name="edgeR: Concatenate Expression Matrices" version="1.0.0">
+<tool id="concatenate_expression_matrices" name="edgeR: Concatenate Expression Matrices" version="1.0.0.b">
     <description>Create a full expression matrix by selecting the desired columns from specific count tables</description>
     
     <macros>
diff -r a4a4c88783ea -r ec951a5017f8 edgeR_Convert_DGE_Table_to_Bedgraph.xml
--- a/edgeR_Convert_DGE_Table_to_Bedgraph.xml	Tue Sep 01 04:59:05 2015 -0400
+++ b/edgeR_Convert_DGE_Table_to_Bedgraph.xml	Tue Sep 01 09:15:07 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-    <tool id="edger_dge_table_to_bedgraph" name="edgeR: Convert 'differentially expressed genes'-table to bedgraph(s)" version="1.0.0">
+    <tool id="edger_dge_table_to_bedgraph" name="edgeR: Convert 'differentially expressed genes'-table to bedgraph(s)" version="1.0.0.b">
     <description>EdgeR's "differentially expressed genes" table to bedgraph(s)</description>
     
     <macros>
@@ -10,7 +10,7 @@
         <requirement type="package" version="1.0.0">edger_dge_table_to_bedgraph</requirement>
     </requirements>
     
-    <command interpreter="python">
+    <command>
         edger_dge_table_to_bedgraph
             -t $cpm_table
             -g $geneset
diff -r a4a4c88783ea -r ec951a5017f8 edgeR_Design_from_Expression_Matrix.xml
--- a/edgeR_Design_from_Expression_Matrix.xml	Tue Sep 01 04:59:05 2015 -0400
+++ b/edgeR_Design_from_Expression_Matrix.xml	Tue Sep 01 09:15:07 2015 -0400
@@ -10,7 +10,7 @@
         <requirement type="package" version="1.0.0">design_matrix_creator</requirement>
     </requirements>
     
-    <command interpreter="python">
+    <command>
         design_matrix_creator
             -c $expression_matrix
             
@@ -123,17 +123,11 @@
 Overview
 --------
 
-Create a design matrix by selecting the desired patients from an
-expression matrix.
+Create a design matrix by selecting the desired patients from an expression matrix.
 
 Input
 -----
 
-**References**
-
-The test data is coming from:  doi: 10.1093/bioinformatics/btt688.
-http://www.ncbi.nlm.nih.gov/pubmed/24319002
-
 @CONTACT@
     </help>
     
diff -r a4a4c88783ea -r ec951a5017f8 edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Tue Sep 01 04:59:05 2015 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Tue Sep 01 09:15:07 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.a">
+<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.b">
     <description>RNA-Seq gene expression analysis using edgeR (R package)</description>
     
     <macros>
@@ -30,7 +30,7 @@
                description="LOCALE has not been set correctly" />
     </stdio>
     
-    <version_command>echo $(R --version | grep version | grep -v GNU) ", EdgeR version" $(R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2&gt; /dev/null | grep -v -i "WARNING: ")</version_command>
+    <version_command>echo $(R --version | grep version | grep -v GNU)", EdgeR version" $(R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2&gt; /dev/null | grep -v -i "WARNING: ")</version_command>
     
     <command>
         R --vanilla --slave -f $R_script '--args
@@ -101,11 +101,6 @@
             
             $output_format_images
             '
-            #if $output_R:
-                > $output_R 
-            #else:
-                > /dev/null
-            #end if
     </command>
     
     <configfiles>
@@ -218,39 +213,43 @@
   dge <- estimateGLMTagwiseDisp(dge,design)
   
   
-  if(output_MDSplot_logFC != "/dev/null") {
-    write("Creating MDS plot (logFC method)",stdout())
-    points <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
+  # hierarchical clustering makes use of the distance of the MDS
+  if(output_MDSplot_logFC != "/dev/null" || output_hierarchical_clustering_plot != "/dev/null") {
+    write("Calculating MDS plot (logFC method)",stdout())
+    mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
     dev.off()# Kill it
     
-    if(output_format_images == "pdf") {
-      pdf(output_MDSplot_logFC,height=14,width=14)
-    } else if(output_format_images == "svg") {
-      svg(output_MDSplot_logFC,height=14,width=14)
-    } else {
-      ## png(output_MDSplot_logFC)
-      ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
+    if(output_MDSplot_logFC != "/dev/null") {  
+      write("Creating MDS plot (logFC method)",stdout())
+      if(output_format_images == "pdf") {
+        pdf(output_MDSplot_logFC,height=14,width=14)
+      } else if(output_format_images == "svg") {
+        svg(output_MDSplot_logFC,height=14,width=14)
+      } else {
+        ## png(output_MDSplot_logFC)
+        ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
+        
+        bitmap(output_MDSplot_logFC,type="png16m",height=7*3,width=7*3)
+      }
       
-      bitmap(output_MDSplot_logFC,type="png16m",height=14,width=14)
-    }
-    
-    
-    diff_x <- abs(max(points\$x)-min(points\$x))
-    diff_y <-(max(points\$y)-min(points\$y))
-    plot(c(min(points\$x),max(points\$x) + 0.45 * diff_x), c(min(points\$y) - 0.05 * diff_y,max(points\$y) + 0.05 * diff_y), main="edgeR logFC-MDS Plot on top 500 genes",type="n", xlab="Leading logFC dim 1", ylab="Leading logFC dim 2")
-    points(points\$x,points\$y,pch=20)
-    text(points\$x, points\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
-    rm(diff_x,diff_y)
-    
-    dev.off()
+      diff_x <- abs(max(mds_distance_logFC\$x)-min(mds_distance_logFC\$x))
+      diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y))
+      plot(c(min(mds_distance_logFC\$x),max(mds_distance_logFC\$x) + 0.45 * diff_x), c(min(mds_distance_logFC\$y) - 0.05 * diff_y,max(mds_distance_logFC\$y) + 0.05 * diff_y), main="edgeR logFC-MDS Plot on top 500 genes",type="n", xlab="Leading logFC dim 1", ylab="Leading logFC dim 2")
+      points(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20)
+      text(mds_distance_logFC\$x, mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
+      rm(diff_x,diff_y)
+      
+      dev.off()
+      }
   }
   
+  
   if(output_MDSplot_bcv != "/dev/null") {
     write("Creating MDS plot (bcv method)",stdout())
     
     ## 1. First create a virtual plot to obtain the desired coordinates
     pdf("bcvmds.pdf")
-    points <- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)))
+    mds_distance_BCV <- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)))
     dev.off()# Kill it
     
     ## 2. Re-plot the coordinates in a new figure with the size and settings.
@@ -262,14 +261,14 @@
       ## png(output_MDSplot_bcv)
       ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
       
-      bitmap(output_MDSplot_bcv,type="png16m",height=14,width=14)
+      bitmap(output_MDSplot_bcv,type="png16m",height=7*3,width=7*3)
     }
     
-    diff_x <- abs(max(points\$x)-min(points\$x))
-    diff_y <- (max(points\$y)-min(points\$y))
-    plot(c(min(points\$x),max(points\$x) + 0.45 * diff_x), c(min(points\$y) - 0.05 * diff_y,max(points\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2")
-    points(points\$x,points\$y,pch=20)
-    text(points\$x, points\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
+    diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x))
+    diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y))
+    plot(c(min(mds_distance_BCV\$x),max(mds_distance_BCV\$x) + 0.45 * diff_x), c(min(mds_distance_BCV\$y) - 0.05 * diff_y,max(mds_distance_BCV\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2")
+    points(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20)
+    text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
     rm(diff_x,diff_y)
     
     dev.off()
@@ -287,7 +286,7 @@
       ## png(output_BCVplot)
       ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
       
-      bitmap(output_BCVplot,type="png16m")
+      bitmap(output_BCVplot,type="png16m",width=10.5*3,height=7*3)
     }
     
     plotBCV(dge, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance")
@@ -303,7 +302,7 @@
   cont <- makeContrasts(contrasts=cont, levels=design)
 
   lrt <- glmLRT(fit, contrast=cont[,1])
-  write(paste("Exporting to file: ",output_count_edgeR,sep=""),stdout())
+  write(paste("Exporting DGE results to file...",output_count_edgeR,sep=""),stdout())
   write.table(file=output_count_edgeR,topTags(lrt,n=nrow(read_counts))\$table,sep="\t",row.names=TRUE,col.names=NA)
   write.table(file=output_cpm,cpm(dge,normalized.lib.sizes=TRUE),sep="\t",row.names=TRUE,col.names=NA)
 
@@ -325,7 +324,7 @@
         ## png(output_MAplot)
         ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
         
-        bitmap(output_MAplot,type="png16m")
+        bitmap(output_MAplot,type="png16m",width=10.5*3,height=7*3)
       }
       
       with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance"))
@@ -345,7 +344,7 @@
         ## png(output_PValue_distribution_plot)
         ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
         
-        bitmap(output_PValue_distribution_plot,type="png16m",width=14,height=14)
+        bitmap(output_PValue_distribution_plot,type="png16m",width=7*3,height=7*3)
       }
       
       expressed_genes <- subset(etable, PValue < 0.99)
@@ -374,7 +373,7 @@
       ## png(output_heatmap_plot)
       ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
       
-      bitmap(output_heatmap_plot,type="png16m",width=10.5)
+      bitmap(output_heatmap_plot,type="png16m",width=10.5*3,height=7*3)
     }
     
     etable2 <- topTags(lrt, n=100)\$table
@@ -384,7 +383,24 @@
     dev.off()
   }
   
-  ##output_hierarchical_clustering_plot = args[13]
+  if(output_hierarchical_clustering_plot != "/dev/null") {
+    if(output_hierarchical_clustering_plot == "pdf") {
+      pdf(output_hierarchical_clustering_plot,width=10.5)
+    } else if(output_hierarchical_clustering_plot == "svg") {
+      svg(output_hierarchical_clustering_plot,width=10.5)
+    } else {
+      ## png(output_hierarchical_clustering_plot)
+      ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
+      
+      bitmap(output_hierarchical_clustering_plot,type="png16m",width=10.5*3,height=7*3)
+    }
+    
+    mds_distance = as.dist(mds_distance_logFC\$distance.matrix)
+    clustering = hclust(mds_distance)
+    plot(clustering,main=paste("Cluster Dendogram on the ",mds_distance_logFC\$top," TopTags",sep="",sub="\ncomplete linkage on logFC MDS distance"))
+    
+    dev.off()
+  }
   
   if(output_RData_obj != "/dev/null") {
     save.image(output_RData_obj)
@@ -411,10 +427,8 @@
             <option value="make_output_BCVplot">BCV-plot</option>
             <option value="make_output_MAplot">MA-plot</option>
             <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option>
-            <option value="make_output_hierarchical_clustering_plot">Hierarchical custering (under contstruction)</option>
+            <option value="make_output_hierarchical_clustering_plot">Hierarchical custering</option>
             <option value="make_output_heatmap_plot">Heatmap</option>
-            
-            <option value="make_output_R_stdout">R stdout</option>
             <option value="make_output_RData_obj">R Data object</option>
         </param>
         
@@ -595,7 +609,7 @@
 Installation
 ------------
 
-This tool requires no specific configurations. The following dependencies are installed automatically:
+This tool requires no specific configuration. The following dependencies will installed automatically:
 
 - R
 - limma
@@ -610,28 +624,6 @@
 - edgeR
     - GPL (&gt;=2)
 
-References
-----------
-
-EdgeR
-^^^^^
-**[1] edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.**
-
-*Mark D. Robinson, Davis J. McCarthy and Gordon K. Smyth* - Bioinformatics (2010) 26 (1): 139-140.
-
-- http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html
-- http://dx.doi.org/10.1093/bioinformatics/btp616
-- http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
-
-Test-data (MCF7)
-^^^^^^^^^^^^^^^^
-**[2] RNA-seq differential expression studies: more sequence or more replication?**
-
-*Yuwen Liu, Jie Zhou and Kevin P. White* - Bioinformatics (2014) 30 (3): 301-304.
-
-- http://www.ncbi.nlm.nih.gov/pubmed/24319002
-- http://dx.doi.org/10.1093/bioinformatics/btt688
-
 @CONTACT@
     </help>
     
diff -r a4a4c88783ea -r ec951a5017f8 test-data/Differential_Gene_Expression/differentially_expressed_genes.tabular.txt
--- a/test-data/Differential_Gene_Expression/differentially_expressed_genes.tabular.txt	Tue Sep 01 04:59:05 2015 -0400
+++ b/test-data/Differential_Gene_Expression/differentially_expressed_genes.tabular.txt	Tue Sep 01 09:15:07 2015 -0400
@@ -1,29 +1,29 @@
 ""	"genes"	"logFC"	"logCPM"	"LR"	"PValue"	"FDR"
-"15"	"RET"	1.94897640107287	13.2940435307943	77.654599543179	1.22730171836821e-18	3.55917498326782e-17
-"24"	"HSPA8"	0.607138087178611	18.9380827005326	16.8408380175314	4.06490891367457e-05	0.000589411792482813
-"12"	"IFI44L"	-0.665544707287885	11.7020333673755	13.7144720204488	0.000212808307971688	0.00205714697705965
-"10"	"MYO18A"	-0.608389235629078	14.1586814058554	10.0030349278008	0.00156282461000764	0.0113304784225554
-"4"	"DDX11"	0.719283453206407	12.4597575302041	9.12036988131984	0.00252778847255745	0.0146611731408332
-"26"	"NR2C2AP"	0.538719097450498	12.9331552590697	7.88314604327009	0.00498976028659176	0.0241171747185268
-"19"	"RASSF3"	-0.322613484306053	12.4964626371138	4.62652086564883	0.0314813398355935	0.130422693604602
-"3"	"DDX17"	-0.202898462175599	16.1804174471336	2.58563106106719	0.107837421983493	0.390910654690163
-"2"	"USP26"	-2.18026172235612	4.27316802151059	2.23964914988384	0.134511497925546	0.433425937760093
-"27"	"INADL"	-0.171517188407227	15.2186072712825	1.67097950802946	0.19612738879992	0.532259040389235
-"21"	"LYSMD3"	-0.195688416211883	13.32535006408	1.62863926869131	0.201891360147641	0.532259040389235
-"16"	"IQCG"	-0.204602031239979	10.1622224199572	1.27895197461613	0.258093988838365	0.623727139692716
-"14"	"KCNAB3"	0.235558773538239	7.85434240586327	0.626910369343036	0.428490880664559	0.920477060517754
-"6"	"SLC35D3"	0.732791849378157	4.62274850327991	0.571072605743573	0.449833005996972	0.920477060517754
-"20"	"FUT8"	-0.101052861033366	15.3006920075591	0.507763042822674	0.476108824405735	0.920477060517754
-"1"	"COMMD10"	0.124183380838805	12.8850203875481	0.427219144496277	0.513356635936627	0.927280503730139
-"9"	"TXLNB"	-0.182677549934781	7.2825391341052	0.332700921323453	0.56407299924751	0.927280503730139
-"28"	"TMEM31"	-0.242966946412951	6.16897757110336	0.313478542290647	0.575553416108362	0.927280503730139
-"7"	"GLOD4"	-0.0680179216917625	13.8710260882794	0.180025725971987	0.671351132981887	0.998117639327786
-"17"	"C20orf118"	0.14522927187254	6.73904801103973	0.160869778108134	0.688356992639853	0.998117639327786
-"22"	"LMOD3"	0.0653797517936461	7.60390982671528	0.0485282387333417	0.825644327378613	1
-"8"	"GIMAP7"	0.278076976843342	4.26623062002702	0.0410800206726094	0.839383539966141	1
-"23"	"HIPK1"	-0.00503549836369412	17.7957744498389	0.00154544013400937	0.968641570543933	1
-"13"	"KHSRP"	-0.00239769805103114	14.7206397592923	0.000263977505255752	0.987037033025321	1
-"11"	"ATG4B"	0.00130641853526229	13.5252482941211	3.53338139831294e-05	0.995257222366413	1
+"15"	"RET"	1.94897640107286	13.2940435307943	77.6545995415986	1.22730171935022e-18	3.55917498611563e-17
+"24"	"HSPA8"	0.607138087178614	18.9380827005326	16.8408380186893	4.06490891119454e-05	0.000589411792123208
+"12"	"IFI44L"	-0.665544707287881	11.7020333673755	13.7144720195324	0.000212808308075529	0.00205714697806344
+"10"	"MYO18A"	-0.608389235629078	14.1586814058554	10.0030349277278	0.00156282461006963	0.0113304784230048
+"4"	"DDX11"	0.719283453206409	12.4597575302041	9.1203698809081	0.00252778847312638	0.014661173144133
+"26"	"NR2C2AP"	0.538719097450497	12.9331552590697	7.88314604309164	0.00498976028708414	0.0241171747209067
+"19"	"RASSF3"	-0.322613484306052	12.4964626371138	4.62652086549247	0.031481339838463	0.130422693616489
+"3"	"DDX17"	-0.202898462175601	16.1804174471336	2.58563106107022	0.107837421983287	0.390910654689415
+"2"	"USP26"	-2.18026172235612	4.27316802151059	2.23964990963176	0.134511431832489	0.433425724793576
+"27"	"INADL"	-0.171517188407228	15.2186072712825	1.67097950803399	0.196127388799313	0.532259040398981
+"21"	"LYSMD3"	-0.195688416211876	13.32535006408	1.62863926866461	0.201891360151338	0.532259040398981
+"16"	"IQCG"	-0.204602031239968	10.1622224199572	1.27895197435303	0.258093988887329	0.623727139811046
+"14"	"KCNAB3"	0.235558773538239	7.85434240586327	0.626910368891663	0.42849088083079	0.920477060511131
+"6"	"SLC35D3"	0.732791849378157	4.62274850327991	0.571073743098566	0.449832554709518	0.920477060511131
+"20"	"FUT8"	-0.10105286103336	15.3006920075591	0.507763042830561	0.476108824402309	0.920477060511131
+"1"	"COMMD10"	0.124183380838807	12.8850203875481	0.427219144492929	0.513356635938278	0.927280503918676
+"9"	"TXLNB"	-0.182677549934781	7.2825391341052	0.332700920948795	0.564072999466928	0.927280503918676
+"28"	"TMEM31"	-0.242966946412956	6.16897757110336	0.313478542098543	0.575553416225385	0.927280503918676
+"7"	"GLOD4"	-0.0680179216917574	13.8710260882794	0.180025725971447	0.671351132982351	0.998117639846733
+"17"	"C20orf118"	0.14522927187254	6.73904801103973	0.16086977771818	0.688356992997747	0.998117639846733
+"22"	"LMOD3"	0.065379751793664	7.60390982671528	0.0485282385969317	0.825644327619727	1
+"8"	"GIMAP7"	0.278076976843342	4.26623062002702	0.0410821671265458	0.839379401017925	1
+"23"	"HIPK1"	-0.0050354983636938	17.7957744498389	0.00154544012787028	0.968641570606185	1
+"13"	"KHSRP"	-0.00239769805103114	14.7206397592923	0.000263977502370949	0.987037033096146	1
+"11"	"ATG4B"	0.00130641853526229	13.5252482941211	3.5333815787908e-05	0.995257222245289	1
 "5"	"PTPN20B"	0	4.09631395702755	0	1	1
 "18"	"GPIHBP1"	0	4.09631395702755	0	1	1
 "25"	"TAS2R39"	0	4.09631395702755	0	1	1
diff -r a4a4c88783ea -r ec951a5017f8 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 01 04:59:05 2015 -0400
+++ b/tool_dependencies.xml	Tue Sep 01 09:15:07 2015 -0400
@@ -7,13 +7,12 @@
     <package name="design_matrix_creator" version="1.0.0">
         <install version="1.0">
             <actions>
-                <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/bin/design_matrix_creator $INSTALL_DIR/bin/</action>
+                <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/bin/design_matrix_creator $INSTALL_DIR/bin/design_matrix_creator</action>
                 <action type="chmod">
                     <file mode="755">$INSTALL_DIR/bin/design_matrix_creator</file>
                 </action>
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>
@@ -22,13 +21,12 @@
     <package name="edger_dge_table_to_bedgraph" version="1.0.0">
         <install version="1.0">
             <actions>
-                <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/bin/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/</action>
+                <action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/bin/edger_dge_table_to_bedgraph $INSTALL_DIR/bin/edger_dge_table_to_bedgraph</action>
                 <action type="chmod">
                     <file mode="755">$INSTALL_DIR/bin/edger_dge_table_to_bedgraph</file>
                 </action>
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>