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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 spack.package import *
class Scalpel(MakefilePackage, SourceforgePackage):
"""Scalpel is a software package for detecting INDELs (INsertions and
DELetions) mutations in a reference genome which has been sequenced
with next-generation sequencing technology.
"""
homepage = "http://scalpel.sourceforge.net/index.html"
sourceforge_mirror_path = "scalpel/scalpel-0.5.4.tar.gz"
license("MIT")
version("0.5.4", sha256="506f731b3886def158c15fd8b74fa98390f304a507d2040972e6b09ddefac8f0")
version("0.5.3", sha256="d45b569fe3aa5934883bc7216c243d53168351c23e020d96a46fa77a1563b65e")
depends_on("perl@5.10.0:")
# bamtools needs to build before the others.
parallel = False
@run_before("install")
def filter_sbang(self):
"""Run before install so that the standard Spack sbang install hook
can fix up the path to the perl|python binary.
"""
with working_dir(self.stage.source_path):
kwargs = {"ignore_absent": True, "backup": False, "string": False}
match = "^#!/usr/bin/env perl"
perl = self.spec["perl"].command
substitute = "#!{perl}".format(perl=perl)
files = [
"FindDenovos.pl",
"scalpel-export",
"scalpel-discovery",
"FindVariants.pl",
"FindSomatic.pl",
]
filter_file(match, substitute, *files, **kwargs)
# Scalpel doesn't actually *have* an install step. The authors
# expect you to unpack the tarball, build it in the resulting
# directory, and add that directory to your PATH. The Perl
# scripts use `FindBin` to discover the directory in which they
# live and they run their own dedicated copies of {bam,sam}tools
# and etc... by explicitly naming the executables in their directory.
#
# Rather than trying to fix their code I just copied the juicy
# bits into prefix.bin. It's not normal, but....
#
def install(self, spec, prefix):
destdir = prefix.bin # see the note above....
mkdirp(destdir)
files = [
"FindSomatic.pl",
"HashesIO.pm",
"MLDBM.pm",
"scalpel-export",
"Utils.pm",
"FindDenovos.pl",
"FindVariants.pl",
"scalpel-discovery",
"SequenceIO.pm",
"Usage.pm",
]
for f in files:
install(f, destdir)
dirs = ["Text", "MLDBM", "Parallel"]
for d in dirs:
install_tree(d, join_path(destdir, d))
install_tree("bamtools-2.3.0/bin", join_path(destdir, "bamtools-2.3.0", "bin"))
install_tree("bamtools-2.3.0/lib", join_path(destdir, "bamtools-2.3.0", "lib"))
mkdirp(join_path(destdir, "bcftools-1.1"))
install("bcftools-1.1/bcftools", join_path(destdir, "bcftools-1.1"))
mkdirp(join_path(destdir, "Microassembler"))
install("Microassembler/Microassembler", join_path(destdir, "Microassembler"))
mkdirp(join_path(destdir, "samtools-1.1"))
install("samtools-1.1/samtools", join_path(destdir, "samtools-1.1"))
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