603569e321
* Style: black 23, skip magic trailing commas * isort should use same line length as black * Fix unused import * Update version of black used in CI * Update new packages * Update new packages
50 lines
1.6 KiB
Python
50 lines
1.6 KiB
Python
# 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 Eagle(MakefilePackage):
|
|
"""EAGLE: Explicit Alternative Genome Likelihood Evaluator"""
|
|
|
|
homepage = "https://github.com/tony-kuo/eagle"
|
|
url = "https://github.com/tony-kuo/eagle/archive/v1.1.2.tar.gz"
|
|
maintainers("snehring")
|
|
|
|
version("1.1.3", sha256="bd510b8eef2de14898cbf417e1c7a30b97ddaba24e5e2834da7b02767362fe3c")
|
|
version("1.1.2", sha256="afe967560d1f8fdbd0caf4b93b5f2a86830e9e4d399fee4a526140431343045e")
|
|
|
|
depends_on("curl")
|
|
depends_on("zlib")
|
|
depends_on("lzma")
|
|
depends_on("htslib")
|
|
|
|
def edit(self, spec, prefix):
|
|
# remove unused gcc flags
|
|
filter_file("$(LFLAGS) $(INCLUDES)", "", "Makefile", string=True)
|
|
|
|
# drop static link to htslib
|
|
filter_file("$(LIBS)", "", "Makefile", string=True)
|
|
|
|
# don't try to build htslib.
|
|
filter_file("all: UTIL HTSLIB", "all: UTIL", "Makefile", string=True)
|
|
|
|
# add htslib link to ldflags
|
|
filter_file("-lcurl", "-lcurl -lhts", "Makefile", string=True)
|
|
|
|
# use spack C compiler
|
|
filter_file("CC=.*", "CC={0}".format(spack_cc), "Makefile")
|
|
|
|
# let the user inject march if they want
|
|
filter_file("-march=native", "", "Makefile", string=True)
|
|
|
|
def install(self, spec, prefix):
|
|
mkdirp(prefix.bin)
|
|
|
|
bins = ["eagle", "eagle-rc", "eagle-nm"]
|
|
|
|
for b in bins:
|
|
install(b, prefix.bin)
|