1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
|
# 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 Snphylo(Package):
"""A pipeline to generate a phylogenetic tree from huge SNP data"""
homepage = "http://chibba.pgml.uga.edu/snphylo/"
url = "https://github.com/thlee/SNPhylo/archive/refs/tags/20180901.tar.gz"
license("GPL-2.0-only")
version("20180901", sha256="46273bcafc8f6cc2465fc524926af7dd122bcc7b7ce1b7c3f5c278111c3a9ddd")
version(
"2016-02-04",
sha256="d9e144021c83dbef97bebf743b92109ad0afcfe70f37c244059b43f11b8a50da",
deprecated=True,
)
depends_on("python", type=("build", "run"))
depends_on("r", type=("build", "run"))
depends_on("r-phangorn", type=("build", "run"))
depends_on("r-gdsfmt", type=("build", "run"))
depends_on("r-snprelate", type=("build", "run"))
depends_on("r-getopt", type=("build", "run"))
depends_on("muscle")
depends_on("phylip")
def install(self, spec, prefix):
install_answer = ["y", "y", "y", "y"]
install_answer_input = "spack-config.in"
with open(install_answer_input, "w") as f:
f.writelines(install_answer)
with open(install_answer_input, "r") as f:
bash = which("bash")
bash("./setup.sh", input=f)
install_tree(".", prefix)
def setup_run_environment(self, env):
env.prepend_path("PATH", self.spec.prefix)
|
