I get the following on OSX 10.10.5
download from
https://github.com/samtools/samtools/releases/download/1.3/samtools-1.3.tar.bz2
<https://github.com/samtools/samtools/releases/download/1.3/samtools-1.3.tar.bz2>
and deploy in /Users/me/Downloads/samtools-1.3/src
cd …/samtools-1.3/src
./configure --prefix=/Users/me/Downloads/samtools-1.3
make
…...
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o
hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o
vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o
cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o
cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o
cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
gcc -pthread -rdynamic -o samtools bam_index.o bam_plcmd.o sam_view.o
bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o
bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o
bam2bcf_indel.o errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o
padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o
bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o
bam_quickcheck.o bam_addrprg.o libbam.a htslib-1.3/libhts.a -lncurses -lm -lz
-ldl
gcc: error: unrecognized command line option '-rdynamic'
make: *** [samtools] Error 1
gcc --version
gcc (MacPorts gcc48 4.8.5_0) 4.8.5
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Any help welcome
Stephane
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