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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
import os
from spack.package import *
class Gapfiller(Package):
"""GapFiller is a stand-alone program for closing gaps within
pre-assembled scaffolds.
Note: A manual download is required for GapFiller.
Spack will search your current directory for the download file.
Alternatively, add this file to a mirror so that Spack can find it.
For instructions on how to set up a mirror, see
https://spack.readthedocs.io/en/latest/mirrors.html"""
homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller"
manual_download = True
version("1.10", md5="54d5e2ada131a1305a66e41c0d380382")
def url_for_version(self, version):
return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format(
os.getcwd(), version.dashed
)
depends_on("perl+threads", type=("build", "run"))
def patch(self):
with working_dir("."):
files = glob.glob("*.pl") + glob.glob("bwa/*.pl")
for file in files:
change = FileFilter(file)
change.filter("usr/bin/perl", "usr/bin/env perl")
change.filter('require "getopts.pl";', "use Getopt::Std;")
change.filter("&Getopts", "getopts")
change.filter("\r", "")
set_executable(file)
def install(self, spec, prefix):
install_tree("bowtie", prefix.bin.bowtie)
install_tree("bwa", prefix.bin.bwa)
install("GapFiller.pl", prefix.bin)
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