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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)
import glob
from spack.package import *
class Hisat2(MakefilePackage):
"""HISAT2 is a fast and sensitive alignment program for mapping
next-generation sequencing reads (whole-genome, transcriptome, and
exome sequencing data) against the general human population (as well as
against a single reference genome)."""
homepage = "https://daehwankimlab.github.io/hisat2/"
url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-source.zip"
license("GPL-3.0-or-later")
version(
"2.2.1",
sha256="48e933330d4d8470d2b3dfe7ec3918f2e98a75f7381891e23b7df1fb4f135eb1",
url="https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download",
extension="zip",
)
version(
"2.2.0",
sha256="0dd55168853b82c1b085f79ed793dd029db163773f52272d7eb51b3b5e4a4cdd",
url="https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-source/download",
extension="zip",
)
version("2.1.0", sha256="89a276eed1fc07414b1601947bc9466bdeb50e8f148ad42074186fe39a1ee781")
variant("sra", default=False, description="Add SRA (Sequence Read Archive) support")
depends_on("perl", type="run")
depends_on("python", type="run")
depends_on("sra-tools", when="+sra")
depends_on("ncbi-vdb", when="+sra")
# patch to get SRA working
patch("sra.patch", when="+sra")
@when("+sra")
def build(self, spec, prefix):
make(
"USE_SRA=1",
"NCBI_NGS_DIR={0}".format(spec["sra-tools"].prefix),
"NCBI_VDB_DIR={0}".format(spec["ncbi-vdb"].prefix),
)
def install(self, spec, prefix):
if spec.satisfies("@:2.1.0"):
install_tree("doc", prefix.doc)
install_tree("example", prefix.example)
install_tree("scripts", prefix.scripts)
if "@:2.2.0" in spec:
install_tree("hisatgenotype_modules", prefix.hisatgenotype_modules)
install_tree("hisatgenotype_scripts", prefix.hisatgenotype_scripts)
mkdirp(prefix.bin)
install("hisat2", prefix.bin)
install("hisat2-align-s", prefix.bin)
install("hisat2-align-l", prefix.bin)
install("hisat2-build", prefix.bin)
install("hisat2-build-s", prefix.bin)
install("hisat2-build-l", prefix.bin)
install("hisat2-inspect", prefix.bin)
install("hisat2-inspect-s", prefix.bin)
install("hisat2-inspect-l", prefix.bin)
install("*.py", prefix.bin)
if "@2.2:" in spec:
install("hisat2-repeat", prefix.bin)
@run_after("install")
def filter_sbang(self):
with working_dir(self.prefix.bin):
pattern = "^#!.*/usr/bin/env python"
repl = "#!{0}".format(self.spec["python"].command.path)
files = ["hisat2-build", "hisat2-inspect"]
for file in files:
filter_file(pattern, repl, *files, backup=False)
pattern = "^#!.*/usr/bin/env perl"
repl = "#!{0}".format(self.spec["perl"].command.path)
files = ["hisat2"]
for file in files:
filter_file(pattern, repl, *files, backup=False)
pattern = "^#!.*/usr/bin/env python3"
repl = "#!{0}".format(self.spec["python"].command.path)
files = glob.glob("*.py")
for file in files:
filter_file(pattern, repl, *files, backup=False)
with working_dir(self.prefix.scripts):
pattern = "^#!.*/usr/bin/perl"
repl = "#!{0}".format(self.spec["perl"].command.path)
files = glob.glob("*.pl")
for file in files:
filter_file(pattern, repl, *files, backup=False)
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