From 47628521b978360ad2252e8826a381e607ca5544 Mon Sep 17 00:00:00 2001
From: snehring <7978778+snehring@users.noreply.github.com>
Date: Mon, 12 Dec 2022 04:31:26 -0600
Subject: delly2: add v1.1.6 (#34411)

---
 var/spack/repos/builtin/packages/delly2/package.py | 27 +++++++++++++++-------
 1 file changed, 19 insertions(+), 8 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/delly2/package.py b/var/spack/repos/builtin/packages/delly2/package.py
index 112d1cd24e..d51b4d09dc 100644
--- a/var/spack/repos/builtin/packages/delly2/package.py
+++ b/var/spack/repos/builtin/packages/delly2/package.py
@@ -4,7 +4,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack.package import *
-from spack.pkg.builtin.boost import Boost
 
 
 class Delly2(MakefilePackage):
@@ -14,19 +13,27 @@ class Delly2(MakefilePackage):
     short-read massively parallel sequencing data.."""
 
     homepage = "https://github.com/dellytools/delly"
+    url = "https://github.com/dellytools/delly/archive/refs/tags/v1.1.6.tar.gz"
     git = "https://github.com/dellytools/delly.git"
+    maintainers = ["snehring"]
 
+    version("1.1.6", sha256="08961e9c81431eb486476fa71eea94941ad24ec1970b71e5a7720623a39bfd2a")
     version("0.9.1", tag="v0.9.1")
     version("2017-08-03", commit="e32a9cd55c7e3df5a6ae4a91f31a0deb354529fc", deprecated=True)
 
     variant("openmp", default=False, description="Build with openmp support")
 
     depends_on("htslib", type=("build", "link"))
-    depends_on("boost", type=("build", "link"))
-    # TODO: replace this with an explicit list of components of Boost,
-    # for instance depends_on('boost +filesystem')
-    # See https://github.com/spack/spack/pull/22303 for reference
-    depends_on(Boost.with_default_variants)
+    depends_on(
+        "boost@:1.78.0+iostreams+filesystem+system+program_options+date_time",
+        when="@:0.9.1",
+        type=("build", "link"),
+    )
+    depends_on(
+        "boost+iostreams+filesystem+system+program_options+date_time",
+        when="@0.9.1:",
+        type=("build", "link"),
+    )
     depends_on("bcftools", type="run")
 
     def edit(self, spec, prefix):
@@ -49,13 +56,17 @@ class Delly2(MakefilePackage):
             makefile.filter(".boost:", "# .boost:")
         else:
             env["EBROOTHTSLIB"] = self.spec["htslib"].prefix
-            filter_file("BUILT_PROGRAMS =.*$", "BUILT_PROGRAMS = src/delly src/dpe", "Makefile")
+            if self.spec.satisfies("@0.9.1"):
+                filter_file(
+                    "BUILT_PROGRAMS =.*$", "BUILT_PROGRAMS = src/delly src/dpe", "Makefile"
+                )
             filter_file("${SUBMODULES}", "", "Makefile", string=True)
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
         with working_dir("src"):
             install("delly", prefix.bin)
-            install("dpe", prefix.bin)
+            if self.spec.satisfies("@0.9.1") or self.spec.satisfies("@2017-08-03"):
+                install("dpe", prefix.bin)
             if self.spec.satisfies("@2017-08-03"):
                 install("cov", prefix.bin)
-- 
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