1 files changed, 54 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/mapsplice2/package.py b/var/spack/repos/builtin/packages/mapsplice2/package.py
new file mode 100644
index 0000000000..0f9f1c1139
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mapsplice2/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2021 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 import *
+
+
+class Mapsplice2(MakefilePackage):
+    """MapSplice is a software for mapping RNA-seq data to reference genome
+       for splice junction discovery that depends only on reference genome,
+       and not on any further annotations."""
+
+    homepage = "http://www.netlab.uky.edu/p/bioinfo/MapSplice2"
+    url = "https://protocols.netlab.uky.edu/~zeng/MapSplice-v2.2.1.zip"
+
+    version(
+        "2.2.1",
+        sha256="4f3c1cb49ba0abcfc952de5946ee0b56db28c51f4f4d4f5abca66b4461ca7d05",
+    )
+
+    patch("Makefile.patch")
+    patch("mapsplice_ebwt.patch")
+
+    depends_on("bowtie")
+    depends_on("ncurses", type="link")
+    depends_on("samtools", type="link")
+    depends_on("python", type="run")
+
+    def edit(self, spec, prefix):
+        for iscan in find(
+            "src",
+            [
+                "SamRec.*",
+                "AlignmentHandler.cpp",
+                "JunctionHandler.cpp",
+                "FusionSamRec.*",
+            ],
+            recursive=True,
+        ):
+            m = FileFilter(iscan)
+            m.filter(r"iscanonical", "iscanonical2")
+
+        for makefile in find(".", "[Mm]akefile", recursive=True):
+            m = FileFilter(makefile)
+            m.filter("g++", "{0}".format(spack_cxx), string=True)
+            m.filter(r"CC =.*", "CC = {0}".format(spack_cc))
+            m.filter(r"CPP =.*", "CPP = {0}".format(spack_cxx))
+            m.filter(r"CXX =.*", "CXX = {0}".format(spack_cxx))
+
+    def install(self, spec, prefix):
+        install("mapsplice.py", prefix)
+        install_tree("bin", prefix.bin)