1 files changed, 0 insertions, 56 deletions
diff --git a/var/spack/repos/builtin/packages/hic-pro/package.py b/var/spack/repos/builtin/packages/hic-pro/package.py
deleted file mode 100644
index e5e1e606d5..0000000000
--- a/var/spack/repos/builtin/packages/hic-pro/package.py
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 2013-2022 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 HicPro(MakefilePackage):
-    """HiC-Pro is a package designed to process Hi-C data,
-    from raw fastq files (paired-end Illumina data)
-    to the normalized contact maps"""
-
-    homepage = "https://github.com/nservant/HiC-Pro"
-    url = "https://github.com/nservant/HiC-Pro/archive/v2.10.0.tar.gz"
-
-    version("2.10.0", sha256="df181ea5c57247caf6b25fd15dfbb03df597ff8c4f57599d88607648bb61f1b7")
-
-    depends_on("bowtie2")
-    depends_on("samtools")
-    depends_on("python+ucs4@2.7:2.8")
-    depends_on("r")
-    depends_on("py-numpy", type=("build", "run"))
-    depends_on("py-scipy", type=("build", "run"))
-    depends_on("py-pysam", type=("build", "run"))
-    depends_on("py-bx-python", type=("build", "run"))
-    depends_on("r-rcolorbrewer", type=("build", "run"))
-    depends_on("r-ggplot2", type=("build", "run"))
-
-    def edit(self, spec, prefix):
-        config = FileFilter("config-install.txt")
-        config.filter("PREFIX =.*", "PREFIX = {0}".format(prefix))
-        config.filter("BOWTIE2 PATH =.*", "BOWTIE2_PATH = {0}".format(spec["bowtie2"].prefix))
-        config.filter("SAMTOOLS_PATH =.*", "SAMTOOLS_PATH = {0}".format(spec["samtools"].prefix))
-        config.filter("R_PATH =.*", "R_RPTH ={0}".format(spec["r"].prefix))
-        config.filter("PYTHON_PATH =.*", "PYTHON_RPTH ={0}".format(spec["python"].prefix))
-
-    def build(self, spec, preifx):
-        make("-f", "./scripts/install/Makefile", "CONFIG_SYS=./config-install.txt")
-        make("mapbuilder")
-        make("readstrimming")
-        make("iced")
-
-    def install(self, spec, prefix):
-        # Patch INSTALLPATH in config-system.txt
-        config = FileFilter("config-system.txt")
-        config.filter("/HiC-Pro_%s" % self.version, "")
-        # Install
-        install("config-hicpro.txt", prefix)
-        install("config-install.txt", prefix)
-        install("config-system.txt", prefix)
-        install_tree("bin", prefix.bin)
-        install_tree("annotation", prefix.annotation)
-        install_tree("doc", prefix.doc)
-        install_tree("scripts", prefix.scripts)
-        install_tree("test-op", join_path(prefix, "test-op"))