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#!/bin/bash
CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
EXTERNAL_DIR=${CURR_DIR}/../external
INSTALL_DIR=${CURR_DIR}/../external/install
if [ -d ${EXTERNAL_DIR}/RapMap ] ; then
rm -fr ${EXTERNAL_DIR}/RapMap
fi
if [ -d ${INSTALL_DIR}/include/rapmap ] ; then
rm -fr ${INSTALL_DIR}/include/rapmap
fi
if [ -d ${INSTALL_DIR}/src/rapmap ] ; then
rm -fr ${INSTALL_DIR}/src/rapmap
fi
mkdir -p ${EXTERNAL_DIR}
curl -k -L https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.7.2.zip -o ${EXTERNAL_DIR}/rapmap.zip
#curl -k -L https://github.com/COMBINE-lab/RapMap/archive/develop-salmon.zip -o ${EXTERNAL_DIR}/rapmap.zip
rm -fr ${EXTERNAL_DIR}/RapMap
unzip ${EXTERNAL_DIR}/rapmap.zip -d ${EXTERNAL_DIR}
#mv ${EXTERNAL_DIR}/RapMap-develop-salmon ${EXTERNAL_DIR}/RapMap
mv ${EXTERNAL_DIR}/RapMap-salmon-v0.7.2 ${EXTERNAL_DIR}/RapMap
mkdir -p ${INSTALL_DIR}/include/rapmap
mkdir -p ${INSTALL_DIR}/src/rapmap
rm ${EXTERNAL_DIR}/RapMap/src/xxhash.c
rm ${EXTERNAL_DIR}/RapMap/include/xxhash.h
cp -r ${EXTERNAL_DIR}/RapMap/external/libdivsufsort.zip ${EXTERNAL_DIR}
cp -r ${EXTERNAL_DIR}/RapMap/src/*.c ${INSTALL_DIR}/src/rapmap
cp -r ${EXTERNAL_DIR}/RapMap/src/*.cpp ${INSTALL_DIR}/src/rapmap
cp -r ${EXTERNAL_DIR}/RapMap/include/tclap ${INSTALL_DIR}/include/rapmap
cp -r ${EXTERNAL_DIR}/RapMap/include/*.h ${INSTALL_DIR}/include/rapmap
cp -r ${EXTERNAL_DIR}/RapMap/include/*.hpp ${INSTALL_DIR}/include/rapmap
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