File: run_pipeline

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file content (58 lines) | stat: -rw-r--r-- 3,848 bytes parent folder | download | duplicates (4)
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Author: Olivier Sallou <osallou@debian.org>
Subject: use default PATH
Description: use tools in path instead of local dirs as upstream
Last-Updated: 2014-08-20
Forwarded: no
--- a/run_mapsembler2_pipeline.sh
+++ b/run_mapsembler2_pipeline.sh
@@ -16,7 +16,7 @@
 f=1 #kind of process (search mode 1=Breadth and 2=Depth)
 x=40 #node length limit
 y=10000 #graph depth limit
-PATH_TOOLS="./tools/" # path were executables mapsembler and phaser are. Leave blank if they are located in a directory located in the PATH environnement variable
+PATH_TOOLS="" # path were executables mapsembler and phaser are. Leave blank if they are located in a directory located in the PATH environnement variable
 #######################################################################
 #################### END HEADER                 #######################
 #######################################################################
@@ -211,20 +211,20 @@
 	if [ $t -gt 2 ]
 	then
 		echo -e "\n"
-		echo -e "\033[31m running $PATH_TOOLS""kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t.json $read_sets -k $k -c $c -t m -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json\033[0m"
-$PATH_TOOLS\kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t.json $read_sets -k $k -c $c -t m -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json
+		echo -e "\033[31m running $PATH_TOOLS""mapsembler2_kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t.json $read_sets -k $k -c $c -t m -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json\033[0m"
+$PATH_TOOLS\mapsembler2_kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t.json $read_sets -k $k -c $c -t m -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json
 		if [ $? -ne 0 ]
 		then
-			echo "there was a problem with kissreads_graph"
+			echo "there was a problem with mapsembler2_kissreads_graph"
 			exit
 		fi
 
 		echo -e "\n"
-		echo -e "\033[31m $PATH_TOOLS""kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json $read_sets -k $k -c $c  -t c -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified_and_covered.json\033[0m"
-$PATH_TOOLS\kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json $read_sets -k $k -c $c -t c -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified_and_covered.json
+		echo -e "\033[31m $PATH_TOOLS""mapsembler2_kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json $read_sets -k $k -c $c  -t c -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified_and_covered.json\033[0m"
+$PATH_TOOLS\mapsembler2_kissreads_graph $prefix_results\_k_$k\_c_$c\_t_$t\_modified.json $read_sets -k $k -c $c -t c -M -o $prefix_results\_k_$k\_c_$c\_t_$t\_modified_and_covered.json
 		if [ $? -ne 0 ]
 		then
-			echo "there was a problem with kissreads_graph"
+			echo "there was a problem with mapsembler2_kissreads_graph"
 			exit
 		fi
 
@@ -232,11 +232,11 @@
 
 	else
 		echo -e "\n"
-		echo -e "\033[31m running $PATH_TOOLS""kissreads $prefix_results\_k_$k\_c_$c\_t_$t.fasta $read_sets -f -o $prefix_results\_coherent_k_$k\_c_$c\_t_$t.fasta -u $prefix_results\_uncoherent_k_$k\_c_$c\_t_$t.fasta\033[0m"
-$PATH_TOOLS\kissreads $prefix_results\_k_$k\_c_$c\_t_$t.fasta $read_sets -k $k -c $c -d $d -f -o $prefix_results\_coherent_k_$k\_c_$c\_t_$t.fasta -u $prefix_results\_uncoherent_k_$k\_c_$c\_t_$t.fasta
+		echo -e "\033[31m running $PATH_TOOLS""mapsembler2_kissreads $prefix_results\_k_$k\_c_$c\_t_$t.fasta $read_sets -f -o $prefix_results\_coherent_k_$k\_c_$c\_t_$t.fasta -u $prefix_results\_uncoherent_k_$k\_c_$c\_t_$t.fasta\033[0m"
+$PATH_TOOLS\mapsembler2_kissreads $prefix_results\_k_$k\_c_$c\_t_$t.fasta $read_sets -k $k -c $c -d $d -f -o $prefix_results\_coherent_k_$k\_c_$c\_t_$t.fasta -u $prefix_results\_uncoherent_k_$k\_c_$c\_t_$t.fasta
 		if [ $? -ne 0 ]
 		then
-			echo "there was a problem with kissreads"
+			echo "there was a problem with mapsembler2_kissreads"
 			exit
 		fi