if [ -z ${CONDA_BUILD+x} ]; then
    source /opt/conda/conda-bld/repeatmasker_1620335938015/work/build_env_setup.sh
fi
#!/bin/bash

RM_DIR=${PREFIX}/share/RepeatMasker
mkdir -p ${PREFIX}/bin
mkdir -p ${RM_DIR}
cp -r * ${RM_DIR}

# configure
cd ${RM_DIR}
perl ./configure -libdir ${RM_DIR}/Libraries -trf_prgm ${PREFIX}/bin/trf  -rmblast_dir ${PREFIX}/bin/ -hmmer_dir ${PREFIX}/bin -abblast_dir ${PREFIX}/bin -crossmatch_dir ${PREFIX}/bin -default_search_engine rmblast


# ----- add tools within the bin ------

# add RepeatMasker
ln -s ${RM_DIR}/RepeatMasker ${PREFIX}/bin/RepeatMasker

# add other tools
RM_OTHER_PROGRAMS="DateRepeats DupMasker ProcessRepeats RepeatProteinMask"
for name in ${RM_OTHER_PROGRAMS} ; do
  ln -s ${RM_DIR}/${name} ${PREFIX}/bin/${name}
done

# add all utils
for name in ${RM_DIR}/util/* ; do
  ln -s $name ${PREFIX}/bin/$(basename $name)
done