shapemapper: add new package (#36282)

var/spack/repos/builtin/packages/bbmap/package.py

@@ -12,7 +12,9 @@ class Bbmap(Package, SourceforgePackage):
     homepage = "https://sourceforge.net/projects/bbmap/"
     sourceforge_mirror_path = "bbmap/BBMap_38.63.tar.gz"
 
+    version("39.01", sha256="98608da50130c47f3abd095b889cc87f60beeb8b96169b664bc9d849abe093e6")
     version("38.63", sha256="089064104526c8d696164aefa067f935b888bc71ef95527c72a98c17ee90a01f")
+    version("37.78", sha256="f2da19f64d2bfb7db4c0392212668b425c96a27c77bd9d88d8f0aea90a193509")
     version("37.36", sha256="befe76d7d6f3d0f0cd79b8a01004a2283bdc0b5ab21b0743e9dbde7c7d79e8a9")
 
     depends_on("java")

var/spack/repos/builtin/packages/shapemapper/package.py

@@ -0,0 +1,48 @@
+# 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 Shapemapper(CMakePackage):
+    """
+    ShapeMapper automates the calculation of RNA structure probing reactivities from mutational
+    profiling (MaP) experiments, in which chemical adducts on RNA are detected as internal
+    mutations in cDNA through reverse transcription and read out by massively parallel sequencing.
+    """
+
+    homepage = "https://github.com/Weeks-UNC/shapemapper2"
+    url = "https://github.com/Weeks-UNC/shapemapper2/releases/download/2.1.5/shapemapper-2.1.5-source-only.tar.gz"
+
+    maintainers("snehring")
+
+    version(
+        "2.1.5",
+        sha256="0846a5d8b5f01d2d039fad4b957df0b6220a8505463f1a410368a1b90d2b227c",
+        url="https://github.com/Weeks-UNC/shapemapper2/releases/download/2.1.5/shapemapper-2.1.5-source-only.tar.gz",
+    )
+
+    depends_on("bowtie2@2.3.0: ^perl+threads", type="run")
+    # hard version dep due to jni
+    depends_on("bbmap@37.78", type="run")
+    depends_on("boost+filesystem+program_options+iostreams+system")
+    depends_on("star@2.5.2:", type="run")
+    depends_on("pv@1.6.0:", type="run")
+    depends_on("python@3.7:", type="run")
+    depends_on("graphviz@2.38.0:", type="run")
+    depends_on("py-scikit-learn@0.18.1:", type="run")
+    depends_on("py-matplotlib@1.5.1:3.3", type="run")
+
+    build_directory = "build"
+
+    def install(self, spec, prefix):
+        for d in ["docs", "internals", "util"]:
+            mkdirp(join_path(prefix, d))
+            install_tree(d, join_path(prefix, d))
+        for f in ["shapemapper", "README.md"]:
+            install(f, prefix)
+
+    def setup_run_environment(self, env):
+        env.prepend_path("PATH", self.prefix)