augustus: fix bam2wig TABIX path (never patched, breaks under Spack) - #6274
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gonzabotmdp wants to merge 1 commit into
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augustus: fix bam2wig TABIX path (never patched, breaks under Spack)#6274gonzabotmdp wants to merge 1 commit into
gonzabotmdp wants to merge 1 commit into
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Summary
auxprogs/bam2wig's own Makefile has:The existing
edit()step already patchesBCFTOOLS/SAMTOOLS/HTSLIBto point at the real Spack-installed prefixes, but never patchesTABIX-- it silently falls back to$HOME/tools/tabix/, which doesn't exist for anyone building via Spack. The actual symptom isbam2wig.c:18:10: fatal error: sam.h: No such file or directory, since without a working-I$(TABIX)there's no path where the bare#include "sam.h"(the old ~2012 flat htslib layout) resolves.Modern htslib nests the same header under
include/htslib/sam.h. SinceTABIXhere is only ever used as an extra-Isearch path (not an actual tabix installation), pointing it at$(HTSLIB)/include/htslibmakes the bare#include "sam.h"resolve correctly without needing a real tabix package at all.Testing
Installed
augustus@3.3.2(abusco@6.1.0dependency,auxprogs/bam2wigis part of the default aux-tools build) with this fix applied, confirmedbam2wigcompiles and links successfully.