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
45
46
47
48
49
50
51
52
53
54
55
56
57
|
# 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 os import unlink
from spack.package import *
class Pasta(PythonPackage):
"""PASTA (Practical Alignment using SATe and Transitivity)"""
homepage = "https://github.com/smirarab/pasta"
git = "https://github.com/smirarab/pasta"
maintainers("snehring")
license("GPL-3.0-or-later")
version("1.9.0", commit="370ae2d21ef461bcb2cef7c20cb5a4a1db7ff99d")
depends_on("python@3:", type=("build", "run"))
depends_on("py-dendropy@4:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("java", type="run")
resource(
name="tools",
git="https://github.com/smirarab/sate-tools-linux",
commit="90fb074d61af554e94d1a67583dd3a80b11417ea",
destination=".",
)
def setup_build_environment(self, env):
tools = join_path(self.prefix, "sate-tools-linux")
env.set("PASTA_TOOLS_DEVDIR", tools)
env.set("PASTA_TOOLS_RUNDIR", self.prefix.bin)
def setup_run_environment(self, env):
env.set("PASTA_TOOLS_RUNDIR", self.prefix.bin)
@run_before("install")
def install_resource(self):
with working_dir(self.stage.source_path):
tools = tools = join_path(self.prefix, "sate-tools-linux")
install_tree("sate-tools-linux", tools)
@run_after("install")
def install_stragglers(self):
# install script negelects to actually copy some things
scripts = join_path(self.stage.source_path, "resources", "scripts")
with working_dir(scripts):
unlink(join_path(self.prefix.bin, "hmmeralign"))
install("hmmeralign", self.prefix.bin)
src_bin = join_path(self.stage.source_path, "bin")
with working_dir(src_bin):
install("treeshrink", self.prefix.bin)
|
