#!/bin/env beesh

SRCURL[0]="http://sourceforge.net/projects/samtools/files/samtools/${PKGVERSION}/samtools-${PKGVERSION}.tar.bz2"

# SRCURL[0]="/src/mariux/beeroot/downloads/samtools-${PKGFULLVERSION}.tar.bz2"

build_in_sourcedir

PREFIX=/usr/local

mee_patch_post() {
    sed -i misc/varfilter.py \
        -e 's,/software/bin/python,/usr/bin/env python,'
}

mee_build_post() {
    bee_build razip
}

mee_install() {
   mkdir -pv ${D}{${BINDIR},${LIBDIR},${INCLUDEDIR}/bam,${MANDIR}/man1}
   
   install -v -m 0755 \
       samtools \
       bcftools/bcftools \
       misc/*.pl \
       misc/{maq2sam-{long,short},md5sum-lite,wgsim} \
       misc/bamcheck \
       misc/varfilter.py \
         ${D}${BINDIR}

   install -v -m 0644 \
       libbam.a \
         ${D}${LIBDIR}

   install -v -m 0644 \
       ${S}/*.h \
          ${D}${INCLUDEDIR}/bam
   
   install -v -m 0644 \
       samtools.1 \
          ${D}${MANDIR}/man1
}