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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
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