jpayne@69: if [ -z ${CONDA_BUILD+x} ]; then
jpayne@69:     source /opt/conda/conda-bld/mummer_1734020773944/work/build_env_setup.sh
jpayne@69: fi
jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: set -xe
jpayne@69: 
jpayne@69: BINARY=mummer
jpayne@69: BINARY_HOME=$PREFIX/bin
jpayne@69: MUMMER_HOME=$PREFIX/opt/mummer-$PKG_VERSION
jpayne@69: 
jpayne@69: mkdir -p $BINARY_HOME
jpayne@69: mkdir -p $MUMMER_HOME
jpayne@69: 
jpayne@69: # cd to location of Makefile and source
jpayne@69: cp -R $SRC_DIR/* $MUMMER_HOME
jpayne@69: 
jpayne@69: cd $MUMMER_HOME
jpayne@69: 
jpayne@69: # One of the Makefiles references a shell script not in the path
jpayne@69: export PATH="$PATH:."
jpayne@69: make CC=$CC CXX=$CXX CPPFLAGS="-O3 -DSIXTYFOURBITS"
jpayne@69: 
jpayne@69: binaries="\
jpayne@69: combineMUMs \
jpayne@69: delta-filter \
jpayne@69: dnadiff \
jpayne@69: exact-tandems \
jpayne@69: mapview \
jpayne@69: mgaps \
jpayne@69: mummer \
jpayne@69: mummerplot \
jpayne@69: nucmer \
jpayne@69: promer \
jpayne@69: repeat-match \
jpayne@69: run-mummer1 \
jpayne@69: run-mummer3 \
jpayne@69: show-aligns \
jpayne@69: show-coords \
jpayne@69: show-diff \
jpayne@69: show-snps \
jpayne@69: show-tiling \
jpayne@69: "
jpayne@69: 
jpayne@69: # patch defined(%hash) out
jpayne@69: # https://github.com/bioconda/bioconda-recipes/issues/1254
jpayne@69: 
jpayne@69: perl -i -pe 's/defined \(%/\(%/' mummerplot
jpayne@69: 
jpayne@69: #Fix escaping symbol @ included in the path to the library (mainly for conda virtual env with galaxy)
jpayne@69: for i in exact-tandems dnadiff mapview mummerplot nucmer promer run-mummer1 run-mummer3; do
jpayne@69:   perl -i -pe 's/(envs\/\_\_.*)(\K\@)/\\@/' $i
jpayne@69: done
jpayne@69: 
jpayne@69: # fix hashbang lines to use conda's perl
jpayne@69: for i in dnadiff mapview mummerplot nucmer promer; do
jpayne@69:   sed -i.bak '1 s|^#!/.*/perl -w$|#!/usr/bin/env perl|g' $MUMMER_HOME/$i
jpayne@69:   rm -rf $MUMMER_HOME/$i.bak
jpayne@69: done
jpayne@69: 
jpayne@69: for i in $binaries; do 
jpayne@69:   # ensure executable and setup symlink for binary
jpayne@69:   chmod +x $MUMMER_HOME/$i
jpayne@69:   ln -s "$MUMMER_HOME/$i" "$BINARY_HOME/$i"
jpayne@69: done
jpayne@69: 
jpayne@69: # clean up
jpayne@69: find $MUMMER_HOME -name *.o -exec rm -f {} \;