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#!/bin/bash
#Copyright inria / irisa (2013)
#
#
#pierre.peterlongo@inria.fr
#
#This software is a computer program whose purpose is performe optimized targeted assembly from reads
#
#This software is governed by the CeCILL license under French law and
#abiding by the rules of distribution of free software. You can use,
#modify and/ or redistribute the software under the terms of the CeCILL
#license as circulated by CEA, CNRS and INRIA at the following URL
#"http:#www.cecill.info".
#
#As a counterpart to the access to the source code and rights to copy,
#modify and redistribute granted by the license, users are provided only
#with a limited warranty and the software's author, the holder of the
#economic rights, and the successive licensors have only limited
#liability.
#
#In this respect, the user's attention is drawn to the risks associated
#with loading, using, modifying and/or developing or reproducing the
#software by the user in light of its specific status of free software,
#that may mean that it is complicated to manipulate, and that also
#therefore means that it is reserved for developers and experienced
#professionals having in-depth computer knowledge. Users are therefore
#encouraged to load and test the software's suitability as regards their
#requirements in conditions enabling the security of their systems and/or
#data to be ensured and, more generally, to use and operate it in the
#same conditions as regards security.
#
#The fact that you are presently reading this means that you have had
#knowledge of the CeCILL license and that you accept its terms.
#######################################################################
#################### HEADER, CHANGE VALUES HERE #######################
#######################################################################
k=29
b=""
Dopt=""
#######################################################################
#################### END HEADER #######################
#######################################################################
function help {
echo "clean_all_tools.sh is a script cleaning for mapsembler2_extremities, mapsembler2_extend and kissreads_graph or kissreads to build mapsembler2_pipeline"
echo "Usage: ./compile_all_tools.sh "
echo "removes all executables and compiled files"
echo "Any further question: read the readme file or contact us: pierre.peterlongo@inria.fr"
}
#######################################################################
#################### GET OPTIONS #######################
#######################################################################
while getopts "h" opt; do
case $opt in
h)
help
exit
;;
\?)
echo "Invalid option: -$OPTARG" >&2
exit 1
;;
:)
echo "Option -$OPTARG requires an argument." >&2
exit 1
;;
esac
done
rm -rf tools
echo "#######################################################################
################## CLEAN MAPSEMBLER2 EXTREMITIES ####################
#######################################################################"
cd mapsembler2_extremities
if [ -d "./build" ]
then
rm -rf build
fi
echo "#######################################################################
#################### CLEAN MAPSEMBLER2 EXTEND #######################
#######################################################################"
if [ -d "./thirdparty/zlib/build" ]
then
rm -rf ./thirdparty/zlib/build/
fi
cd ../mapsembler2_extend
make clean
cd ..
echo "#######################################################################
###################### CLEAN KISSREADSGRAPH #########################
#######################################################################"
cd kissreads_graph
make clean
cd ..
echo "#######################################################################
######################## CLEAN KISSREADS ############################
#######################################################################"
cd kissreads
make clean
cd ..
echo "Cleaning is done"
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