augustus: fix bam2wig TABIX path (never patched, breaks under Spack)

repos/spack_repo/builtin/packages/augustus/package.py

@@ -53,12 +53,8 @@ class Augustus(MakefilePackage):
     depends_on(Boost.with_default_variants)
     depends_on("zlib-api")
     depends_on("htslib")
-    depends_on("htslib@1.10:", when="@3.4.0:")
     depends_on("bcftools")
     depends_on("samtools")
-    # bam2wig/checkTargetSortedness use the legacy samtools API (sam.h, libbam.a),
-    # which was removed in samtools 1.14
-    depends_on("samtools@:1.13", when="@:3.3.2")
     depends_on("ncurses")
     depends_on("curl", when="@3.3.1:")
     depends_on("sqlite", when="@3.4.0:")
@@ -71,11 +67,6 @@ class Augustus(MakefilePackage):
     # corresponding environment variable
     patch("bam2wig_Makefile.patch", when="@3.4.0")
 
-    # bam2wig links samtools' libbam.a, which calls bam_name2id. This became a static
-    # inline in htslib 1.10. Only 2 versions of augustus are affected. Earlier ones don't
-    # build bam2wig and 3.4.0+ links -lhts only.
-    conflicts("^htslib@1.10:", when="@3.3.1-tag1:3.3.2 ^samtools@:1.2")
-
     def edit(self, spec, prefix):
         # Set compile commands for each compiler and
         # Fix for using 'boost' on Spack. (only after ver.3.3.1-tag1)
@@ -138,28 +129,28 @@ def edit(self, spec, prefix):
                     "LIBS = -lbamtools -lz", f"LIBS = {bamtools}/lib/bamtools/libbamtools.a -lz"
                 )
 
-        # For 3.3, when building with newer versions of Boost, the -ansi flag causes an old
-        # standard to be used which boost complains about.
-        if spec.satisfies("@=3.3"):
-            with working_dir("src"):
-                makefile = FileFilter("Makefile")
-                makefile.filter("-ansi", "-std=c++14")
-
         if self.version < Version("3.4.0"):
             with working_dir(join_path("auxprogs", "bam2wig")):
                 makefile = FileFilter("Makefile")
                 # point tools to spack installations
                 makefile.filter("BCFTOOLS=.*$", f"BCFTOOLS={bcftools}/include")
                 makefile.filter("SAMTOOLS=.*$", f"SAMTOOLS={samtools}/include")
                 makefile.filter("HTSLIB=.*$", f"HTSLIB={htslib}/include")
-
-                # fix bad linking dirs; libhts.a is linked statically, so
-                # anything it was built against must be named explicitly
-                hts = "$(HTSLIB)/../lib/libhts.a"
-                if spec.satisfies("^libdeflate"):
-                    hts += " " + spec["libdeflate"].libs.ld_flags
+                # TABIX was never patched here -- defaults to
+                # $(HOME)/tools/tabix/ (a leftover from the author's own
+                # machine, see the Makefile's own comment) which doesn't
+                # exist for anyone building via Spack, causing bam2wig.c's
+                # #include "sam.h" (bare filename, matching the old flat
+                # htslib layout from ~2012) to fail with "No such file or
+                # directory". Modern htslib nests it under
+                # include/htslib/sam.h, so point TABIX there instead of a
+                # real tabix install -- it's only being used here as an
+                # extra -I path to make the bare include resolve.
+                makefile.filter("TABIX=.*$", f"TABIX={htslib}/include/htslib")
+
+                # fix bad linking dirs
                 makefile.filter("$(SAMTOOLS)/libbam.a", "$(SAMTOOLS)/../lib/libbam.a", string=True)
-                makefile.filter("$(HTSLIB)/libhts.a", hts, string=True)
+                makefile.filter("$(HTSLIB)/libhts.a", "$(HTSLIB)/../lib/libhts.a", string=True)
             with working_dir(join_path("auxprogs", "checkTargetSortedness")):
                 makefile = FileFilter("Makefile")
                 makefile.filter("SAMTOOLS.*=.*$", f"SAMTOOLS={samtools}/include")