seqfu: new package (#44445)

* Add seqfu

---------

Co-authored-by: dialvarezs <dialvarezs@users.noreply.github.com>

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

@@ -0,0 +1,32 @@
+# 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)
+
+from spack.package import *
+
+
+class Seqfu(Package):
+    """seqfu - Sequece Fastx Utilities"""
+
+    homepage = "https://github.com/telatin/seqfu2"
+    url = "https://github.com/telatin/seqfu2/archive/refs/tags/v1.20.3.tar.gz"
+
+    license("GPL-3.0", checked_by="dialvarezs")
+
+    version("1.20.3", sha256="1b287b99f3f1ac7045f4d551e781d6780ce168ba8e0a7bfaa0f5490f32e15938")
+
+    depends_on("nim@2", type="build")
+    depends_on("zlib", type="build")
+
+    patch("wno_incompatible_pointer_types.patch", when="%gcc@14:")
+
+    def setup_build_environment(self, env):
+        env.set("NIMBLE_DIR", ".nimble")
+
+    def install(self, spec, prefix):
+        nimble = Executable("nimble")
+        nimble("install", "-y", "--depsOnly")
+
+        make(parallel=False)
+        install_tree("bin", join_path(prefix, "bin"))

var/spack/repos/builtin/packages/seqfu/wno_incompatible_pointer_types.patch

@@ -0,0 +1,13 @@
+diff --git a/Makefile b/Makefile
+index 287bb7c..7fb9434 100644
+--- a/Makefile
++++ b/Makefile
+@@ -7,7 +7,7 @@ SCRIPTS=./scripts
+ SOURCE=./src
+ DATA=./data
+ VERSION := $(shell grep version seqfu.nimble  | grep  -o "[0-9]\\+\.[0-9]\\+\.[0-9]\\+")
+-NIMPARAM :=  --gc:orc -d:NimblePkgVersion=$(VERSION) -d:release --opt:speed 
++NIMPARAM :=  --gc:orc -d:NimblePkgVersion=$(VERSION) -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types"
+ TARGETS=$(BIN)/seqfu $(BIN)/fu-msa $(BIN)/fu-primers $(BIN)/dadaist2-mergeseqs $(BIN)/fu-shred $(BIN)/fu-homocomp $(BIN)/fu-multirelabel $(BIN)/fu-index $(BIN)/fu-cov $(BIN)/fu-16Sregion  $(BIN)/fu-nanotags  $(BIN)/fu-orf  $(BIN)/fu-sw  $(BIN)/fu-virfilter  $(BIN)/fu-tabcheck $(BIN)/byteshift $(BIN)/SeqCountHelper $(BIN)/fu-secheck
+ PYTARGETS=$(BIN)/fu-split $(BIN)/fu-pecheck $(BIN)/fu-readtope
+