py-panaroo, py-edlib, and py-intbitset: new packages (#31452)

3 files changed, 78 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-edlib/package.py b/var/spack/repos/builtin/packages/py-edlib/package.py
new file mode 100644
index 0000000000..991b82b799
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-edlib/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2022 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 PyEdlib(PythonPackage):
+    """Lightweight, super fast library for sequence
+       alignment using edit (Levenshtein) distance."""
+
+    homepage = "https://pypi.org/project/edlib/"
+    pypi     = "edlib/edlib-1.3.9.tar.gz"
+
+    version('1.3.9', sha256='64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-intbitset/package.py b/var/spack/repos/builtin/packages/py-intbitset/package.py
new file mode 100644
index 0000000000..0c3049bd66
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-intbitset/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2022 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 PyIntbitset(PythonPackage):
+    """The intbitset library provides a set implementation to store sorted
+    unsigned integers either 32-bits integers or an infinite range with fast
+    set operations implemented via bit vectors in a Python C extension for
+    speed and reduced memory usage."""
+
+    homepage = "https://github.com/inveniosoftware/intbitset"
+    pypi     = "intbitset/intbitset-3.0.1.tar.gz"
+
+    version('3.0.1', sha256='f1e6d03c6729922a223c51849df65b9e916e625aefb911784e7f9acd4c207d53')
+
+    depends_on('py-setuptools',   type='build')
diff --git a/var/spack/repos/builtin/packages/py-panaroo/package.py b/var/spack/repos/builtin/packages/py-panaroo/package.py
new file mode 100644
index 0000000000..9e3c2f455a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-panaroo/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2022 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 PyPanaroo(PythonPackage):
+    """A Bacterial Pangenome Analysis Pipeline"""
+
+    homepage = "https://gtonkinhill.github.io/panaroo"
+    url      = "https://github.com/gtonkinhill/panaroo/archive/refs/tags/v1.2.10.tar.gz"
+
+    version('1.2.10', sha256='066e5cd96b59918fa4fcd2dc12c92a273457ee17e2fe55576657c793566e948e')
+
+    depends_on('python@3.6.0:',   type=('build', 'run'))
+    depends_on('py-setuptools',   type='build')
+    depends_on('py-biopython',    type=('build', 'run'))
+    depends_on('py-numpy',        type=('build', 'run'))
+    depends_on('py-scipy',        type=('build', 'run'))
+    depends_on('py-matplotlib',   type=('build', 'run'))
+    depends_on('py-plotly',       type=('build', 'run'))
+    depends_on('py-dendropy',     type=('build', 'run'))
+    depends_on('py-scikit-learn', type=('build', 'run'))
+    depends_on('py-networkx',     type=('build', 'run'))
+    depends_on('py-gffutils',     type=('build', 'run'))
+    depends_on('py-edlib',        type=('build', 'run'))
+    depends_on('py-joblib',       type=('build', 'run'))
+    depends_on('py-tqdm',         type=('build', 'run'))
+    depends_on('py-intbitset',    type=('build', 'run'))
+    depends_on('cdhit',           type=('build', 'run'))
+    depends_on('prokka',          type=('build', 'run'))
+    depends_on('prank',           type=('build', 'run'))
+    depends_on('mafft',           type=('build', 'run'))
+    depends_on('clustal-omega',   type=('build', 'run'))
+    depends_on('mash',            type=('build', 'run'))