--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/orthologs/ucsb_hamster/ucsb_hamster.sh	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,67 @@
+#!/bin/sh
+
+#############################################
+# 				UCSB HAMSTER				#
+# 											#
+# Executes Hamster with given XML parameter #
+#############################################
+
+#the name of the script is here
+#script="/home/osiris/galaxy-dist/tools/osiris/orthologs/ucsb_hamster/hamstrsearch_local-hmmer3.pl"
+script="hamstrsearch_local-hmmer3.pl"
+ 
+
+
+#Variables input from xml
+# 1 - Sequence input file
+# 2 - Proteins Results Output file
+# 3 - cds Results Output file
+# 4 - Screen Log
+# 5 - Species Name
+# 6 - Whether to use -est flag (if D) or not (if P)
+# 7 - Core ortholog name
+# 8 - Base path for local core orthologs
+# 9 - Base path for local reference blast database
+#10 - Reference genome
+
+input=$1
+proteins=$2
+cdsfile=$3
+screenlog=$4
+species=$5
+datatype=$6
+core=$7
+corepath=$8
+blastpath=$9
+genome=${10}
+
+echo "ucsb_hamster.sh script parameters" >> $screenlog
+echo "Core ortholog name is $core " >> $screenlog
+echo "Reference genome name is $genome " >> $screenlog
+echo "Species name is $species " >> $screenlog
+echo "Datatype $datatype " >> $screenlog
+
+#set flag based on input
+if [ $datatype = "P" ];
+        then
+            	estflag="-protein"
+        else
+            	estflag="-est"
+        fi
+
+# First copy hmm's to working directory
+# Currently copies from Data directory
+mkdir $core
+mkdir $core/hmm_dir
+cp -r $corepath/* ./$core/
+echo "cp $corepath/hmm_dir/* ./$core/hmm_dir/" >> $screenlog
+cp -r $corepath/hmm_dir/* ./$core/hmm_dir/
+
+# Currently copies from data directory
+mkdir $genome
+cp $blastpath/* ./$genome/
+
+# Now call the actual Hamster Script
+#$script -sequence_file=$input $estflag -taxon=$species -hmmset=$core -refspec=$genome -galaxyout=$proteins -2galaxyout=$cdsfile >> $screenlog 2>log.txt
+$script -sequence_file=$input $estflag -taxon=$species -hmmset=$core -refspec=$genome -galaxyout=$proteins -2galaxyout=$cdsfile >> $screenlog
+