How to compile without system zlib?

[mjsteinbaugh]

Hi @alexdobin , I'm trying to write an install recipe for STAR that uses a version pinned external zlib library, rather than using system zlib. I've tried a couple of approaches without success (e.g. setting CPPFLAGS, LDFLAGS, LDLIBS, etc.; adjusting htslib Makefile).

My install script is here, for reference:
https://github.com/acidgenomics/koopa/blob/main/lang/bash/include/install/common/shared/star.sh

It seems like this is an issue that keeps popping up, without a solution other than installing system zlib, which may not be an option on some Linux instances without admin permissions:

• STAR compilation error #1563
• Failed installation in AWS Ubuntu 20 LTS #1379
• Install error #631
• Installation Error in Ubuntu 14.04 #142

Potentially related htslib issues:

• Compiling error: cram/cram.h samtools/htslib#1074
• HTSlib should prefer its own headers when being compiled samtools/htslib#347

Any advice would be much appreciated!

Best,
Mike

[mjsteinbaugh]

Also it looks like this htslib unbundle pull request would fix my issue, as I can install htslib successfully outside of the one bundled with STAR: #1586

[mjsteinbaugh]

Also, here's how bioconda is currently unbundling htslib, which removes the system zlib requirement:
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/star/patches/0002-donotuse_own_htslib.patch