From 4cc5e9cac68ba278e33f16f76b48f66bdeb0b470 Mon Sep 17 00:00:00 2001
From: snehring <7978778+snehring@users.noreply.github.com>
Date: Mon, 12 Jun 2023 03:05:44 -0500
Subject: ltr-retriever 2.9.4 (#38300)

---
 .../builtin/packages/ltr-retriever/package.py      | 10 +++++++-
 .../repos/builtin/packages/py-tesorter/package.py  | 29 ++++++++++++++++++++++
 2 files changed, 38 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/py-tesorter/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/ltr-retriever/package.py b/var/spack/repos/builtin/packages/ltr-retriever/package.py
index 3d1c9c5645..5d5fd52004 100644
--- a/var/spack/repos/builtin/packages/ltr-retriever/package.py
+++ b/var/spack/repos/builtin/packages/ltr-retriever/package.py
@@ -15,6 +15,9 @@ class LtrRetriever(Package):
     homepage = "https://github.com/oushujun/LTR_retriever"
     url = "https://github.com/oushujun/LTR_retriever/archive/v2.8.7.tar.gz"
 
+    maintainers("snehring")
+
+    version("2.9.4", sha256="a9f4668113d2d75ab97cd85b456f11b00afd4876848a8ef099622ec0d9e505e7")
     version("2.8.7", sha256="29ca6f699c57b5e964aa0ee6c7d3e1e4cd5362dadd789e5f0e8c82fe0bb29369")
 
     depends_on("perl", type="run")
@@ -22,6 +25,7 @@ class LtrRetriever(Package):
     depends_on("hmmer@3.1b2:", type="run")
     depends_on("cdhit", type="run")
     depends_on("repeatmasker", type="run")
+    depends_on("py-tesorter", type="run", when="@2.9.4:")
 
     def install(self, spec, prefix):
         filter_file(r"BLAST\+=.*", "BLAST+=%s" % spec["blast-plus"].prefix.bin, "paths")
@@ -29,8 +33,12 @@ class LtrRetriever(Package):
             "RepeatMasker=.*", "RepeatMasker=%s" % spec["repeatmasker"].prefix.bin, "paths"
         )
         filter_file("HMMER=.*", "HMMER=%s" % spec["hmmer"].prefix.bin, "paths")
-        filter_file("CDHIT=.*", "CDHIT=%s" % spec["cdhit"].prefix, "paths")
+        filter_file("CDHIT=.*", "CDHIT=%s" % spec["cdhit"].prefix.bin, "paths")
         filter_file("BLAST=.*", "", "paths")
+        if spec.satisfies("@2.9.4:"):
+            filter_file(
+                "^TEsorter=.*$", "TEsorter={}".format(spec["py-tesorter"].prefix.bin), "paths"
+            )
 
         mkdirp(prefix.opt)
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/py-tesorter/package.py b/var/spack/repos/builtin/packages/py-tesorter/package.py
new file mode 100644
index 0000000000..d324cef55f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-tesorter/package.py
@@ -0,0 +1,29 @@
+# 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 PyTesorter(PythonPackage):
+    """
+    TEsorter is coded for LTR_retriever to classify long terminal repeat
+    retrotransposons (LTR-RTs) at first. It can also be used to
+    classify any other transposable elements (TEs), including
+    Class I and Class II elements which are covered by the
+    REXdb database.
+    """
+
+    homepage = "https://github.com/zhangrengang/TEsorter"
+    url = "https://github.com/zhangrengang/TEsorter/archive/refs/tags/v1.4.6.tar.gz"
+
+    maintainers("snehring")
+
+    version("1.4.6", sha256="c6952c98fa78d0084742fd6c7d2d1204d36db103c3cbeb19e52093cd9d311523")
+
+    depends_on("py-biopython", type=("build", "run"))
+    depends_on("py-xopen", type=("build", "run"))
+
+    depends_on("hmmer@3.3:", type="run")
+    depends_on("blast-plus", type="run")
-- 
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