py-ipyrad (#37160)

* Adding py-ipyrad for testing

* py-ipyrad: placating flake8

* py-ipyrad: adding version 0.9.90, fixing hard coded path.

* py-ipyrad: use join_path instead of hard coded linux path

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* py-ipyrad: Removing unneeded dependencies

* py-ipyrad: Readded future (see ipyrad setup.py)

* py-ipyrad: Switch to an anchored link in the docs

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* py-ipyrad: Removed patch decorator

---------

Co-authored-by: snehring <snehring@iastate.edu>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

1 files changed, 49 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-ipyrad/package.py b/var/spack/repos/builtin/packages/py-ipyrad/package.py
new file mode 100644
index 0000000000..1419f75bfa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-ipyrad/package.py
@@ -0,0 +1,49 @@
+# 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 PyIpyrad(PythonPackage):
+    """An interactive toolkit for assembly and analysis of restriction-site
+    associated genomic data sets (e.g., RAD, ddRAD, GBS) for population
+    genetic and phylogenetic studies."""
+
+    homepage = "https://github.com/dereneaton/ipyrad"
+
+    url = "https://github.com/dereneaton/ipyrad/archive/refs/tags/0.9.85.tar.gz"
+
+    version("0.9.90", sha256="8b95aa3bae30da15baba90abb03176932411ff708c54d5e4481b811cceb8a4a8")
+    version("0.9.85", sha256="17b07466531655db878919e426743ac649cfab2e92c06c4e45f76ee1517633f9")
+
+    depends_on("py-setuptools", type="build")
+
+    # Dependencies found at
+    # https://ipyrad.readthedocs.io/en/master/3-installation.html#details-dependencies
+    depends_on("bedtools2", type=("build", "run"))
+    depends_on("bwa", type=("build", "run"))
+    depends_on("muscle", type=("build", "run"))
+    depends_on("py-notebook", type=("build", "run"))
+    depends_on("samtools", type=("build", "run"))
+    depends_on("vsearch", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-pandas", type=("build", "run"))
+    depends_on("py-h5py", type=("build", "run"))
+    depends_on("py-numba", type=("build", "run"))
+    depends_on("py-ipyparallel", type=("build", "run"))
+    depends_on("py-pysam", type=("build", "run"))
+    depends_on("py-cutadapt", type=("build", "run"))
+    depends_on("py-requests", type=("build", "run"))
+    depends_on("py-future", type=("build", "run"))
+
+    def patch(self):
+        # ipyrad/core/Parallel.py assumes that ipcluster will always be
+        # in the python root
+        filter_file(
+            r"^IPCLUSTER_BIN\s*=.*$",
+            'IPCLUSTER_BIN = "{}"'.format(self.spec["py-ipyparallel"].prefix.bin.ipcluster),
+            join_path("ipyrad", "core", "Parallel.py"),
+        )