--- a/defuse.xml	Fri Jan 06 16:06:17 2012 -0600
+++ b/defuse.xml	Fri Jan 04 13:29:03 2013 -0600
@@ -1,7 +1,10 @@
-<tool id="defuse" name="DeFuse" version="1.2">
+<tool id="defuse" name="DeFuse" version="1.5">
  <description>identify fusion transcripts</description>
  <requirements>
-  <requirement type="binary"></requirement>
+  <requirement type="package" version="0.5.0">defuse</requirement>
+  <requirement type="package">bowtie</requirement>
+  <requirement type="package">blat</requirement>
+  <requirement type="package">fatotwobit</requirement>
  </requirements>
   <command interpreter="command"> /bin/bash $shscript </command>
  <inputs>
@@ -69,7 +72,7 @@
       </when>  <!-- history -->
   </conditional>  <!-- refGenomeSource -->
   <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files"/>
-  <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
+  <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
  </inputs>
  <configfiles>
   <configfile name="defuse_config">
@@ -91,15 +94,7 @@
 #try
 $ref_dict['source_directory']
 #except
-#try
-## Try to find the defuse source dir in the galaxy tool path
-#import Cheetah.FileUtils
-#set $toolpath = '/'.join([$__root_dir__,'tools','defuse'])
-#set $defuse = $Cheetah.FileUtils.findFiles($toolpath,['defuse.pl'],[],['tools','external','include','em','data'])[0]
-$defuse.replace('/scripts/defuse.pl','')
-#except
-${__root_dir__}/tools/defuse/defuse
-#end try
+__DEFUSE_PATH__
 #end try
 
 # Directory where you want your dataset
@@ -159,37 +154,37 @@
 #try
 $ref_dict['bowtie_bin']
 #except
-/soft/bowtie/0.12.7/bowtie
+__BOWTIE_BIN__
 #end try
 bowtie_build_bin = #slurp
 #try
 $ref_dict['bowtie_build_bin']
 #except
-/soft/bowtie/0.12.7/bowtie-build
+__BOWTIE_BUILD_BIN__
 #end try
 blat_bin = #slurp
 #try
 $ref_dict['blat_bin']
 #except
-/soft/blat/34/bin/blat
+__BLAT_BIN__
 #end try
 fatotwobit_bin = #slurp
 #try
 $ref_dict['fatotwobit_bin']
 #except
-/soft/blat/34/bin/faToTwoBit
+__FATOTWOBIT_BIN__
 #end try
 r_bin = #slurp
 #try
 $ref_dict['r_bin']
 #except
-/project/sdml-sles11-weblocal/R-2.12.1/bin/R
+__R_BIN__
 #end try
 rscript_bin = #slurp
 #try
 $ref_dict['rscript_bin']
 #except
-/project/sdml-sles11-weblocal/R-2.12.1/bin/Rscript
+__RSCRIPT_BIN__
 #end try
 
 #raw
@@ -499,14 +494,12 @@
 #!/bin/bash
 ## define some things for cheetah proccessing
 #set $ds = chr(36)
+#set $amp = chr(38)
 #set $gt = chr(62)
 #set $lt = chr(60)
 #set $echo_cmd = 'echo'
 ## Find the defuse.pl in the galaxy tool path
 #import Cheetah.FileUtils
-#set $toolpath = '/'.join([$__root_dir__,'tools','defuse'])
-#set $defuse = $Cheetah.FileUtils.findFiles($toolpath,['defuse.pl'],[],['tools','external','include','em','data'])[0]
-#set $get_reads = $Cheetah.FileUtils.findFiles($toolpath,['get_reads.pl'],[],['tools','external','include','em','data'])[0]
 ## declare a bash function for converting a results tsv into html with links to the get_reads output files
 results2html() {
   rlts=${ds}1
@@ -531,10 +524,21 @@
     for i in `awk '${ds}1 ~ /[1-9][0-9]*/{print ${ds}1}' ${ds}rlts`;
       do fn=cluster_${ds}{i}_reads.txt;
       pn=${ds}_EFP/${ds}fn;
-      perl $get_reads -c $defuse_config -o output_dir -i ${ds}i ${gt} ${ds}pn;
+      perl \${DEFUSE_PATH}/scripts/get_reads.pl -c $defuse_config -o output_dir -i ${ds}i ${gt} ${ds}pn;
     done
   fi
 }
+## substitute pathnames into config file
+if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
+if `grep __SAMTOOLS_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} SAMTOOLS_BIN=`which samtools`;then sed -i'.tmp' "s#__SAMTOOLS_BIN__#\${SAMTOOLS_BIN}#" $defuse_config; fi
+if `grep __BOWTIE_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi
+if `grep __BOWTIE_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi
+if `grep __BLAT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
+if `grep __FATOTWOBIT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
+if `grep __R_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
+if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi
+
+
 ## copy config to output
 cp $defuse_config $config_txt
 ## make a data_dir  and ln -s the input fastq
@@ -549,7 +553,7 @@
 mkdir -p output_dir
 #end if
 ## run defuse.pl
-perl $defuse -c $defuse_config -d data_dir -o output_dir  -p 8
+perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -d data_dir -o output_dir  -p 8
 ## copy primary results to output datasets
 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
 if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi