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HTSlib is already installed in the cgpbigwig container into the /opt/wtsi-cgp area with all the relevant headers etc (see end for hts listings).
When setting up the new image build in this project I attempted to use the various environment variables to direct to this installed copy, but was unable to get the header linking to work.
Please can the Makefile be altered to support use of an installed htslib?
/opt/wtsi-cgp/bin/htsfile
/opt/wtsi-cgp/include/htslib
/opt/wtsi-cgp/include/htslib/bgzf.h
/opt/wtsi-cgp/include/htslib/cram.h
/opt/wtsi-cgp/include/htslib/faidx.h
/opt/wtsi-cgp/include/htslib/hfile.h
/opt/wtsi-cgp/include/htslib/hts.h
/opt/wtsi-cgp/include/htslib/hts_defs.h
/opt/wtsi-cgp/include/htslib/hts_endian.h
/opt/wtsi-cgp/include/htslib/hts_log.h
/opt/wtsi-cgp/include/htslib/hts_os.h
/opt/wtsi-cgp/include/htslib/kbitset.h
/opt/wtsi-cgp/include/htslib/kfunc.h
/opt/wtsi-cgp/include/htslib/khash.h
/opt/wtsi-cgp/include/htslib/khash_str2int.h
/opt/wtsi-cgp/include/htslib/klist.h
/opt/wtsi-cgp/include/htslib/knetfile.h
/opt/wtsi-cgp/include/htslib/kseq.h
/opt/wtsi-cgp/include/htslib/ksort.h
/opt/wtsi-cgp/include/htslib/kstring.h
/opt/wtsi-cgp/include/htslib/regidx.h
/opt/wtsi-cgp/include/htslib/sam.h
/opt/wtsi-cgp/include/htslib/synced_bcf_reader.h
/opt/wtsi-cgp/include/htslib/tbx.h
/opt/wtsi-cgp/include/htslib/thread_pool.h
/opt/wtsi-cgp/include/htslib/vcf.h
/opt/wtsi-cgp/include/htslib/vcf_sweep.h
/opt/wtsi-cgp/include/htslib/vcfutils.h
/opt/wtsi-cgp/lib/libhts.a
/opt/wtsi-cgp/lib/libhts.so
/opt/wtsi-cgp/lib/libhts.so.1.9
/opt/wtsi-cgp/lib/libhts.so.2
/opt/wtsi-cgp/lib/pkgconfig/htslib.pc
/opt/wtsi-cgp/libexec/htslib
/opt/wtsi-cgp/libexec/htslib/hfile_gcs.so
/opt/wtsi-cgp/libexec/htslib/hfile_libcurl.so
/opt/wtsi-cgp/share/man/man1/htsfile.1
@drjsanger
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