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# Copyright 2013-2024 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 Igv(Package):
"""The Integrative Genomics Viewer (IGV) is a high-performance visualization
tool for interactive exploration of large, integrated genomic datasets.
It supports a wide variety of data types, including array-based and
next-generation sequence data, and genomic annotations."""
homepage = "https://software.broadinstitute.org/software/igv/home"
url = "https://data.broadinstitute.org/igv/projects/downloads/2.8/IGV_2.8.0.zip"
maintainers("snehring")
version("2.16.2", sha256="489d34ed4e807a3d32a3720f11248d2ddf1e21d264b06bea44fbe1ccb74b3aa2")
version("2.12.3", sha256="c87a109deb35994e1b28dee80b5acfd623ec3257f031fcd9cfce008cd32a4cf2")
version("2.8.0", sha256="33f3ac57017907b931f90c35b63b2de2e4f8d2452f0fbb5be39d30288fc9b2c6")
depends_on("java@11:", type="run")
variant("igvtools", default=False, description="Include igvtools")
def url_for_version(self, version):
url = "https://data.broadinstitute.org/igv/projects/downloads/{0}/IGV_{1}.zip"
return url.format(version.up_to(2), version)
def install(self, spec, prefix):
install_tree("lib", prefix.lib)
mkdirp(prefix.bin)
install("igv.args", prefix)
files = ["igv.sh", "igv_hidpi.sh"]
if "+igvtools" in spec:
files.extend(["igvtools", "igvtools_gui", "igvtools_gui_hidpi"])
for f in files:
filter_file("^prefix=.*$", "prefix=" + prefix, f)
filter_file(" java ", " {0} ".format(spec["java"].prefix.bin.java), f)
set_executable(f)
install(f, prefix.bin)
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