seacr: new package @1.4-b2 (#42677)

* seacr: new package @1.4-b2

* Update var/spack/repos/builtin/packages/seacr/package.py

Co-authored-by: Alec Scott <hi@alecbcs.com>

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <hi@alecbcs.com>

1 files changed, 33 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/seacr/package.py b/var/spack/repos/builtin/packages/seacr/package.py
new file mode 100644
index 0000000000..fafe5e6c9d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/seacr/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2024 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 Seacr(Package):
+    """SEACR (Sparse Enrichment Analysis for CUT&RUN) is intended to call peaks and
+    enriched regions from sparse CUT&RUN or chromatin profiling data in which the
+    background is dominated by zeros"""
+
+    homepage = "https://github.com/FredHutch/SEACR"
+    git = "https://github.com/FredHutch/SEACR.git"
+
+    license("GPL-2.0-only", checked_by="A-N-Other")
+
+    version("1.4-b2", tag="v1.4-beta.2", commit="5179a70494eb129fcb1d640177de73f6509654e7")
+    version("1.3", tag="v1.3", commit="5a0efe59f06fb17cf9d34d415bb0c1a1f7a77a3c", preferred=True)
+
+    # Dependencies as per the README.md
+    depends_on("r", type="run")
+    depends_on("bedtools2", type="run")
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        script_name = f"SEACR_{self.version.up_to(2)}"
+        os.chmod(f"{script_name}.sh", 0o755)
+        install(f"{script_name}.sh", prefix.bin.SEACR)
+        install(f"{script_name}.R", prefix.bin)