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spack/var/spack/repos/builtin/packages/igvtools/package.py

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copyrights: update all files with license headers for 2021 - [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files - [x] update all licensed files to say 2013-2021 using `spack license update-copyright-year` - [x] appease mypy with some additions to package.py that needed for oneapi.py
2021-01-02 15:10:28 +08:00
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers - remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
new package: igvtools (#6974)
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#
relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers - remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
new package: igvtools (#6974)
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from spack import *
import os
class Igvtools(Package):
"""IGVTools suite of command-line utilities for preprocessing data
files"""
homepage = "https://software.broadinstitute.org/software/igv/home"
url = "http://data.broadinstitute.org/igv/projects/downloads/2.3/igvtools_2.3.98.zip"
checksums: use sha256 checksums everywhere We'd like to use a consistent checksum scheme everywhere so that we can: a) incorporate archive checksums into our specs and have a consistent hashing algorithm across all specs. b) index mirrors with a consistent type of checksum, and not one that is dependent on how spack packages are written. - [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
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version('2.3.98', sha256='07027c179f25960bab9919f255c0f8e08f0861861ac6dc02d92be8313e0316a4')
new package: igvtools (#6974)
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depends_on('java@8:')
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = 'igvtools.jar'
install(jar_file, prefix.bin)
install_tree('genomes', prefix.genomes)
# Set up a helper script to call java on the jar file,
# explicitly codes the path for java and the jar file.
script_sh = join_path(os.path.dirname(__file__), "igvtools.sh")
install_tree, copy_tree can install into existing directory structures (#8289) Replace use of `shutil.copytree` with `copy_tree` and `install_tree` functions in `llnl.util.filesystem`. - `copy_tree` copies without setting permissions. It should be used to copy files around in the build directory. - `install_tree` copies files and sets permissions. It should be used to copy files into the installation directory. - `install` and `copy` are analogous single-file functions. - add more extensive tests for these functions - update packages to use these functions.
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script = prefix.bin.igvtools
install(script_sh, script)
new package: igvtools (#6974)
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set_executable(script)
# Munge the helper script to explicitly point to java and the
# jar file.
igvtools: fixed query on jdk instead of java (#12195)
2019-07-31 20:49:51 +08:00
java = spec['java'].prefix.bin.java
new package: igvtools (#6974)
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kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
filter_file('^java', java, script, **kwargs)
filter_file(jar_file, join_path(prefix.bin, jar_file),
script, **kwargs)
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