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diff --git a/var/spack/repos/builtin/packages/hicup/package.py b/var/spack/repos/builtin/packages/hicup/package.py
new file mode 100644
index 0000000000..daf3f5da39
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hicup/package.py
@@ -0,0 +1,55 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class Hicup(Package):
+    """HiCUP: a bioinformatics pipeline for processing Hi-C data"""
+
+    homepage = "https://stevenwingett.github.io/HiCUP"
+    url = "https://github.com/StevenWingett/HiCUP/archive/refs/tags/v0.9.2.tar.gz"
+    git = "https://github.com/StevenWingett/HiCUP.git"
+
+    license("LGPL-3.0-only", checked_by="A-N-Other")
+
+    version("0.9.2", sha256="7f9f65669d14fd2499afc4ac87735834b57b8f30b8e5785c4b406ec206cf9d2a")
+    version("0.8.3", sha256="e2381c2c45e0d79a6d1a2d9a8358b3efe8da727112d262cb0122132012266368")
+    version("combinations", branch="combinations")
+
+    variant("bowtie2", description="Use bowtie2 aligner", default=True)
+    variant("bowtie", description="Use bowtie aligner", default=False)
+
+    depends_on("pandoc", type="run")
+    depends_on("perl", type="run")
+    depends_on("perl-math-round", type="run")
+    depends_on("r", type="run")
+    depends_on("r-stringi@1.7.8:", type="run")
+    depends_on("r-markdown", type="run")
+    depends_on("r-tidyverse", type="run")
+    depends_on("r-plotly", type="run")
+    depends_on("samtools@0.1.18:", type="run")
+    # variant dependencies
+    depends_on("bowtie2", type="run", when="+bowtie2")
+    depends_on("bowtie", type="run", when="+bowtie")
+
+    def edit(self, spec, prefix):
+        grep = which("grep")
+        chmod = which("chmod")
+        perl_files = grep("-lRr", "#!/usr/bin/perl", ".").splitlines()
+        for f in perl_files:
+            filter_file("/usr/bin/perl", self.spec["perl"].command.path, f, backup=False)
+            filter_file("$Bin", "$RealBin", f, backup=False)
+            chmod("+x", f)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install("hicup*", prefix.bin)
+        if self.spec.satisfies("@combinations"):
+            install("Misc/get_captured_reads", prefix.bin)
+        else:
+            install("Misc/hicup_capture", prefix.bin)
+        install("Conversion/hicup2*", prefix.bin)
+        install_tree("r_scripts", prefix.bin.r_scripts)