New package: py-kneaddata (#43310)

1 files changed, 35 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-kneaddata/package.py b/var/spack/repos/builtin/packages/py-kneaddata/package.py
new file mode 100644
index 0000000000..6be478c15d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-kneaddata/package.py
@@ -0,0 +1,35 @@
+# 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 PyKneaddata(PythonPackage):
+    """
+    Quality control tool on metagenomic and metatranscriptomic sequencing data,
+    especially data from microbiome experiments
+    """
+
+    homepage = "https://github.com/biobakery/kneaddata"
+    pypi = "kneaddata/kneaddata-0.12.0.tar.gz"
+
+    version("0.12.0", sha256="b211bf973ea50cc89dd5935761ca3b101d422cfb62b215aae08f5ed92a624a58")
+
+    maintainers("Pandapip1")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("trimmomatic@0.33", type=("build", "run"))
+    depends_on("bowtie2@2.2:", type=("build", "run"))
+    depends_on("python", type=("build", "run"))
+    depends_on("java", type=("build", "run"))
+
+    variant("bam", default=True, description="Enable support for input files in BAM format")
+    depends_on("samtools", when="+bam", type=("build", "run"))
+
+    variant("trf", default=True, description="Enable support for Tandem Repeats Finder")
+    depends_on("trf", when="+trf", type=("build", "run"))
+
+    variant("fastqc", default=True, description="Enable support for FastQC")
+    depends_on("fastqc", when="+fastqc", type=("build", "run"))