1 files changed, 50 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/ucsc-bedgraphtobigwig/package.py b/var/spack/repos/builtin/packages/ucsc-bedgraphtobigwig/package.py
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index 0000000000..ccb84f38ea
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+++ b/var/spack/repos/builtin/packages/ucsc-bedgraphtobigwig/package.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2023 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 UcscBedgraphtobigwig(Package):
+    """Convert a bedGraph file to bigWig format."""
+
+    homepage = "http://hgdownload.cse.ucsc.edu/admin/exe/"
+    url = "https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v445.src.tgz"
+
+    version("449", sha256="b5a86863d6cfe2120f6c796a13b1572ad05b22622f6534b95c9d26ccbede09b7")
+    version("445", sha256="c7abb5db6a5e16a79aefcee849d2b59dbc71ee112ca1e41fea0afb25229cf56c")
+
+    depends_on("libpng")
+    depends_on("libuuid")
+    depends_on("gmake")
+    depends_on("openssl")
+    depends_on("zlib")
+    # This package has known issues installing with the latest MySQL because
+    # MySQL removed the type my_bool, while mariadb didn't.
+    # https://groups.google.com/a/soe.ucsc.edu/g/genome/c/mIT6fe9l99g
+    depends_on("mysql-client")
+    conflicts("mysql@8.0.0:")
+
+    def setup_build_environment(self, env):
+        env.set("MYSQLLIBS", "-lmysqlclient")
+        env.set("L", "-lssl")
+        env.set("BINDIR", "bin")
+
+    def install(self, spec, prefix):
+        with working_dir("kent/src/lib"):
+            make()
+        with working_dir("kent/src/htslib"):
+            make()
+        with working_dir("kent/src/jkOwnLib"):
+            make()
+        with working_dir("kent/src/hg/lib"):
+            make()
+        with working_dir("kent/src/hg/lib"):
+            make()
+        with working_dir("kent/src/utils/bedGraphToBigWig"):
+            mkdirp(prefix.bin)
+            mkdirp("bin")
+            make()
+            make("install")
+            install("bin/bedGraphToBigWig", prefix.bin)