New packages: libbigwig, methyldackel (#33273)

* libbigwig: adding new package libbigwig
* methyldackel: adding new package methyldackel
* libbigwig: tighten up curl variant

2 files changed, 66 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/libbigwig/package.py b/var/spack/repos/builtin/packages/libbigwig/package.py
new file mode 100644
index 0000000000..9b6819b7a7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libbigwig/package.py
@@ -0,0 +1,26 @@
+# 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 Libbigwig(CMakePackage):
+    """A C library for reading/parsing local and remote bigWig and bigBed files."""
+
+    homepage = "https://github.com/dpryan79/libBigWig"
+    url = "https://github.com/dpryan79/libBigWig/archive/refs/tags/0.4.7.tar.gz"
+    maintainers = ["snehring"]
+
+    version("0.4.7", sha256="8e057797011d93fa00e756600898af4fe6ca2d48959236efc9f296abe94916d9")
+
+    variant("curl", default=True, description="Build with curl support")
+
+    depends_on("curl", when="+curl")
+
+    def cmake_args(self):
+        args = []
+        if self.spec.satisfies("~curl"):
+            args.append("-DWITH_CURL=OFF")
+        return args
diff --git a/var/spack/repos/builtin/packages/methyldackel/package.py b/var/spack/repos/builtin/packages/methyldackel/package.py
new file mode 100644
index 0000000000..6e943c4c3d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/methyldackel/package.py
@@ -0,0 +1,40 @@
+# 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 Methyldackel(MakefilePackage):
+    """MethylDackel (formerly named PileOMeth, which was a temporary name
+    derived due to it using a PILEup to extract METHylation metrics) will
+    process a coordinate-sorted and indexed BAM or CRAM file containing
+    some form of BS-seq alignments and extract per-base methylation
+    metrics from them.
+    """
+
+    homepage = "https://github.com/dpryan79/MethylDackel"
+    url = "https://github.com/dpryan79/MethylDackel/archive/refs/tags/0.6.1.tar.gz"
+    maintainers = ["snehring"]
+
+    version("0.6.1", sha256="eeb1da4c830bcd9f3e6663a764947d957c41337643069524a4b545812fcf4819")
+
+    depends_on("htslib@1.11:")
+    depends_on("libbigwig")
+    depends_on("curl")
+
+    def edit(self, spec, prefix):
+        filter_file(r"^prefix \?=.*$", "prefix = " + spec.prefix, "Makefile")
+        filter_file(
+            "$(LIBBIGWIG)",
+            join_path(spec["libbigwig"].prefix.lib64, "libBigWig.a"),
+            "Makefile",
+            string=True,
+        )
+        filter_file(
+            "-IlibBigWig",
+            "-I" + spec["libbigwig"].prefix.include.libbigwig,
+            "Makefile",
+            string=True,
+        )