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# 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 symlink
from spack.package import *
class Homer(Package):
"""Software for motif discovery and next generation sequencing analysis"""
homepage = "http://homer.ucsd.edu/homer"
url = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.1.zip"
license("GPL-3.0-only")
version("4.11.1", sha256="80d1cd00616729894017b24a36a2ef81f9cde8bd364e875aead1e0cfb500c82b")
version("4.9.1", sha256="ad1303b0b0400dc8a88dbeae1ee03a94631977b751a3d335326c4febf0eec3a9")
depends_on("perl", type=("build", "run"))
depends_on("r-biocgenerics", type="run")
depends_on("r-biocparallel", type="run")
depends_on("r-edger", type="run")
depends_on("r-deseq2", type="run")
variant("data", default=False, description="Download genome data packages")
def install(self, spec, prefix):
# initialize homer directories
basedir = join_path(prefix.lib, "homer")
mkdirp(basedir)
install_tree(".", basedir)
# symlink bin so it is included in the PATH
symlink(join_path(basedir, "bin"), prefix.bin)
# override homer base directory in configure script
filter_file(
"my $homeDir = $1;",
'my $homeDir = "{0}";'.format(basedir),
"configureHomer.pl",
string=True,
)
# compile/prepare binaries and perl scripts with the correct paths
perl = which("perl")
perl("configureHomer.pl", "-local")
# download extra data if requested
if "+data" in spec:
perl("configureHomer.pl", "-install", "-all")
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