chexmix: new package (#38441)

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>

2 files changed, 52 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/chexmix/chexmix.sh b/var/spack/repos/builtin/packages/chexmix/chexmix.sh
new file mode 100644
index 0000000000..b83bce6e58
--- /dev/null
+++ b/var/spack/repos/builtin/packages/chexmix/chexmix.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the chexmix jar file
+java -jar chexmix.jar "$@"
diff --git a/var/spack/repos/builtin/packages/chexmix/package.py b/var/spack/repos/builtin/packages/chexmix/package.py
new file mode 100644
index 0000000000..6654102f4f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/chexmix/package.py
@@ -0,0 +1,49 @@
+# 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)
+
+import os
+
+from spack.package import *
+
+
+class Chexmix(Package):
+    """ChExMix: the ChIP-exo mixture model. ChExMix aims to characterize protein-DNA binding
+    subtypes in ChIP-exo experiments."""
+
+    homepage = "http://mahonylab.org/software/chexmix"
+    url = "https://github.com/seqcode/chexmix/releases/download/v0.51/chexmix.v0.51.jar"
+
+    # The naming of the .jar files is inconsistent on GitHub. Until this is resolved, downloads
+    # that don't match the above url spec will need to be renamed - see rename_versions().
+    version(
+        "0.52",
+        url="https://github.com/seqcode/chexmix/releases/download/v0.52/chexmix.v0.52.public.jar",
+        sha256="7f856921b6071092cfcf226e4f99d9ab80587cf05502b41d00b8e5e16ccbfcdd",
+        expand=False,
+    )
+
+    depends_on("java@8:", type="run")
+    depends_on("meme", type="run")
+
+    @run_before("install")
+    def rename_versions(self):
+        if self.version == Version("0.52"):
+            os.rename("chexmix.v0.52.public.jar", "chexmix.v0.52.jar")
+
+    def install(self, spec, prefix):
+        # install .jar file
+        mkdirp(prefix.bin)
+        jar_file = "chexmix.v{0}.jar".format(self.version)
+        install(jar_file, prefix.bin)
+        # create a helper script to launch the .jar
+        script_sh = join_path(os.path.dirname(__file__), "chexmix.sh")
+        script = prefix.bin.chexmix
+        install(script_sh, script)
+        set_executable(script)
+        # set the helper script to explicitly point to java and the .jar file
+        java = self.spec["java"].prefix.bin.java
+        kwargs = {"ignore_absent": False, "backup": False, "string": False}
+        filter_file("^java", java, script, **kwargs)
+        filter_file("chexmix.jar", join_path(prefix.bin, jar_file), script, **kwargs)