apps/SAMtools/install.sh: fix install procedure

apps/SAMtools/install.sh

@@ -4,8 +4,38 @@ source ../build_env.sh
 SAMTOOLS_VERSION=1.5
 curl -k -L https://sourceforge.net/projects/samtools/files/samtools/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2/download -o samtools-${SAMTOOLS_VERSION}.tar.bz2
 tar xvf samtools-${SAMTOOLS_VERSION}.tar.bz2
-rm samtools-${SAMTOOLS_VERSION}.tar.bz2
+rm -f samtools-${SAMTOOLS_VERSION}.tar.bz2
 mv samtools-${SAMTOOLS_VERSION} ${SAMTOOLS_VERSION}
 cd ${SAMTOOLS_VERSION}
 ./configure
 make
+mkdir -p bin share/man share/man1 misc/
+prefix=$(pwd)
+exec_prefix=$prefix
+bindir=$exec_prefix/bin
+datarootdir=$prefix/share
+mandir=$datarootdir/man
+man1dir=$mandir/man1
+MKDIR_P="mkdir -p"
+INSTALL="install -p"
+INSTALL_DATA="$INSTALL -m 644"
+INSTALL_DIR="$MKDIR_P -m 755"
+INSTALL_MAN=$INSTALL_DATA
+INSTALL_PROGRAM=$INSTALL
+INSTALL_SCRIPT=$INSTALL_PROGRAM
+PROGRAMS=samtools
+MISC_PROGRAMS=" \
+misc/ace2sam misc/maq2sam-long misc/maq2sam-short \
+misc/md5fa misc/md5sum-lite misc/wgsim"
+MISC_SCRIPTS=" \
+misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
+misc/interpolate_sam.pl misc/novo2sam.pl \
+misc/plot-bamstats misc/psl2sam.pl \
+misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl \
+misc/soap2sam.pl \
+misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl"
+$($INSTALL_DIR $bindir $misc_bindir $man1dir)
+$($INSTALL_PROGRAM $PROGRAMS $bindir)
+$($INSTALL_PROGRAM $MISC_PROGRAMS $misc_bindir)
+$($INSTALL_SCRIPT $MISC_SCRIPTS $misc_bindir)
+$($INSTALL_MAN samtools.1 misc/wgsim.1 $man1dir)