script.sh

#!/bin/bash
set -xeuo pipefail
IFS=$'\n\t'

# git clone https://github.com/cloudflare/zlib &
[ -d "zlib-1.2.8" ] || curl -L https://github.com/cloudflare/zlib/archive/v1.2.8.tar.gz | tar zx  &
# git clone https://github.com/ebiggers/libdeflate.git &
[ -d "libdeflate-1.0" ] || curl -L https://github.com/ebiggers/libdeflate/archive/v1.0.tar.gz | tar zx &
# git clone https://github.com/samtools/htslib.git &
[ -d "htslib-1.8" ] || curl -L https://github.com/samtools/htslib/releases/download/1.8/htslib-1.8.tar.bz2 | tar jx &
# git clone https://github.com/samtools/samtools.git &
[ -d "samtools-1.8" ] || curl -L https://github.com/samtools/samtools/releases/download/1.8/samtools-1.8.tar.bz2 | tar jx &
[ -d "bcftools-1.8" ] || curl -L https://github.com/samtools/bcftools/releases/download/1.8/bcftools-1.8.tar.bz2 | tar jx &
# git clone https://github.com/jkbonfield/io_lib.git &
[ -d "xz-5.2.4" ] || curl -L https://tukaani.org/xz/xz-5.2.4.tar.gz | tar zx &
[ -d "bzip2-1.0.6" ] || curl -L http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz | tar zx &
[ -d "io_lib-1.14.9" ] || curl -L https://github.com/jkbonfield/io_lib/releases/download/io_lib-1-14-9/io_lib-1.14.9.tar.gz | tar zx &

# curl is a bit harder, it has dependencies... probably the system one is fine
# [ -d "curl-7.60.0" ] || curl -L https://curl.haxx.se/download/curl-7.60.0.tar.gz | tar zx &

wait

INSTALL="$PWD/install"

# I try to avoid the .so's so that there is not fooling with LD_LIBRARY_PATH
# avoiding -j on the libtool projects

# LZMA
(
cd "xz-5.2.4"
# this uses libtool, so install it to get rid of the munge
./configure --prefix="$PWD"/install
make clean
make
make install
# hide libtool annoyingness
rm install/lib/*.so* install/lib/*.la
)

(
cd "bzip2-1.0.6"
make clean
make -j4
)

(
cd "zlib-1.2.8"
./configure
make clean
make libz.a -j4
)

(
cd "libdeflate-1.0"
make clean
make libdeflate.a -j4
)

(
cd "htslib-1.8"
env CPPFLAGS="-I$PWD/../libdeflate-1.0" LDFLAGS="-L$PWD/../libdeflate-1.0 -L$PWD/../xz-5.2.4/install/lib/ -L$PWD/../bzip2-1.0.6/ -L$PWD/../zlib-1.2.8/" ./configure --prefix="$INSTALL" --with-libdeflate 
make clean
# forcing static link makes the libhts.so want -fPIC. But we can fake it.
make && true
touch libhts.so
make -j4
make install
rm "$INSTALL"/lib/*.so*
)

(
cd "samtools-1.8"
env LDFLAGS="-L../libdeflate-1.0 -L../xz-5.2.4/install/lib/ -L../bzip2-1.0.6/ -L../zlib-1.2.8/" ./configure --prefix="$INSTALL" --without-curses --with-htslib=../htslib-1.8
make clean
make -j4
make install
)

(
cd "bcftools-1.8"
# dependency on libgsl, probably would be good to have an up to date one of them for perf
env LDFLAGS="-L../libdeflate-1.0 -L../xz-5.2.4/install/lib/ -L../bzip2-1.0.6/ -L../zlib-1.2.8/" ./configure --prefix="$INSTALL" --with-htslib=../htslib-1.8 --enable-libgsl
make clean
make -j4
make install
)

(
cd "io_lib-1.14.9"
env LDFLAGS="-L$PWD/../xz-5.2.4/install/lib/ -L$PWD/../bzip2-1.0.6/ -L$PWD/../zlib-1.2.8/" ./configure --prefix="$INSTALL" --enable-shared=no
make clean
make -j4
make install
rm "$INSTALL"/lib/*.la
)

echo
echo "Check that there are no bad dependencies here:"

echo; echo "tabix"; ldd "$INSTALL"/bin/tabix
echo; echo "samtools"; ldd "$INSTALL"/bin/samtools
echo; echo "scramble"; ldd "$INSTALL"/bin/scramble
# ldd /bin/* | sort | uniq

A script for compiling samtools and scramble while trying to avoid system libraries (because they are old or slow)