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

# Copyright 2013-2022 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 Kaiju(MakefilePackage):
    """Kaiju is a program for the taxonomic classification
    of high-throughput sequencing reads."""

    homepage = "https://github.com/bioinformatics-centre/kaiju"
    url = "https://github.com/bioinformatics-centre/kaiju/archive/v1.6.2.zip"

    version("1.6.2", sha256="2685fed7e27ddeb26530fd60a4b388f2d5f3e29aaa79f8e2e6abcbac64075db8")

    build_directory = "src"

    depends_on("perl-io-compress", type="run")
    depends_on("py-htseq", type="run")

    def edit(self, spec, prefix):
        # Replace ftp:// with https://
        makedb = FileFilter("util/makeDB.sh")
        makedb.filter("ftp://", "https://", string=True)

    def install(self, spec, prefix):
        install_tree("bin", prefix.bin)
Update copyright year to 2022 2022-01-13 03:21:41 +08:00			`# Copyright 2013-2022 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 2018-10-08 04:52:23 +08:00			`# Spack Project Developers. See the top-level COPYRIGHT file for details.`
A new pacakge: Kaiju. (#8111) * A new package: kaiju. * Replace ftp:// with https://. 2018-05-15 00:07:00 +08:00			`#`
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 2018-10-08 04:52:23 +08:00			`# SPDX-License-Identifier: (Apache-2.0 OR MIT)`

refactor: packages import `spack.package` explicitly (#30404) Explicitly import package utilities in all packages, and corresponding fallout. This includes: * rename `spack.package` to `spack.package_base` * rename `spack.pkgkit` to `spack.package` * update all packages in builtin, builtin_mock and tutorials to include `from spack.package import ` update spack style * ensure packages include the import * automatically add the new import and remove any/all imports of `spack` and `spack.pkgkit` from packages when using `--fix` * add support for type-checking packages with mypy when SPACK_MYPY_CHECK_PACKAGES is set in the environment * fix all type checking errors in packages in spack upstream * update spack create to include the new imports * update spack repo to inject the new import, injection persists to allow for a deprecation period Original message below: As requested @adamjstewart, update all packages to use pkgkit. I ended up using isort to do this, so repro is easy: ```console $ isort -a 'from spack.pkgkit import ' --rm 'spack' ./var/spack/repos/builtin/packages//package.py $ spack style --fix ``` There were several line spacing fixups caused either by space manipulation in isort or by packages that haven't been touched since we added requirements, but there are no functional changes in here. * [x] add config to isort to make sure this is maintained going forward 2022-05-29 00:55:44 +08:00			`from spack.package import *`
A new pacakge: Kaiju. (#8111) * A new package: kaiju. * Replace ftp:// with https://. 2018-05-15 00:07:00 +08:00

			`class Kaiju(MakefilePackage):`
			`"""Kaiju is a program for the taxonomic classification`
			`of high-throughput sequencing reads."""`

			`homepage = "https://github.com/bioinformatics-centre/kaiju"`
			`url = "https://github.com/bioinformatics-centre/kaiju/archive/v1.6.2.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 2019-10-11 13:44:41 +08:00			`version("1.6.2", sha256="2685fed7e27ddeb26530fd60a4b388f2d5f3e29aaa79f8e2e6abcbac64075db8")`
A new pacakge: Kaiju. (#8111) * A new package: kaiju. * Replace ftp:// with https://. 2018-05-15 00:07:00 +08:00
			`build_directory = "src"`

			`depends_on("perl-io-compress", type="run")`
			`depends_on("py-htseq", type="run")`

			`def edit(self, spec, prefix):`
			`# Replace ftp:// with https://`
			`makedb = FileFilter("util/makeDB.sh")`
			`makedb.filter("ftp://", "https://", string=True)`

			`def install(self, spec, prefix):`
			`install_tree("bin", prefix.bin)`