diff --git a/apps/SAMtools/install.sh b/apps/SAMtools/install.sh index cc954e015fc2078f5133b8ee932727fbd46ad81d..08b15363f1733a5507e468fbec24a3af21002eb1 100644 --- a/apps/SAMtools/install.sh +++ b/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)