spack/var/spack/repos/builtin/packages/bedtools2/package.py

# 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 Bedtools2(Package):
    """Collectively, the bedtools utilities are a swiss-army knife of
    tools for a wide-range of genomics analysis tasks. The most
    widely-used tools enable genome arithmetic: that is, set theory
    on the genome."""

    homepage = "https://github.com/arq5x/bedtools2"
    url = "https://github.com/arq5x/bedtools2/archive/v2.30.0.tar.gz"

    version("2.31.0", sha256="183cf9a96aabc50ef4bd557a53fd01557a123c05a0dc87651371878f357439ec")
    version("2.30.0", sha256="c575861ec746322961cd15d8c0b532bb2a19333f1cf167bbff73230a7d67302f")
    version("2.29.2", sha256="bc2f36b5d4fc9890c69f607d54da873032628462e88c545dd633d2c787a544a5")
    version("2.27.1", sha256="edcac089d84e63a51f85c3c189469daa7d42180272130b046856faad3cf79112")
    version("2.27.0", sha256="e91390b567e577d337c15ca301e264b0355441f5ab90fa4f971622e3043e0ca0")
    version("2.26.0", sha256="15db784f60a11b104ccbc9f440282e5780e0522b8d55d359a8318a6b61897977")
    version("2.25.0", sha256="159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb")
    version("2.23.0", sha256="9dacaa561d11ce9835d1d51e5aeb092bcbe117b7119663ec9a671abac6a36056")

    depends_on("zlib")
    depends_on("bzip2", when="@2.29:")
    depends_on("xz", when="@2.29:")
    depends_on("python", type="build")

    patch("bedtools-gcc13.patch", level=1, when="@2.27:%gcc@13:")

    def install(self, spec, prefix):
        make("prefix=%s" % prefix, "install")
license year bump (#34921) * license bump year * fix black issues of modified files * mypy * fix 2021 -> 2023 2023-01-19 06:30:17 +08:00			`# Copyright 2013-2023 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.`
Add package for bedtools2 (#1572) Add package for bedtools2, with support for v2.25.0 and v2.26.0. 2016-09-21 19:23:03 +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 *`
Add package for bedtools2 (#1572) Add package for bedtools2, with support for v2.25.0 and v2.26.0. 2016-09-21 19:23:03 +08:00

			`class Bedtools2(Package):`
			`"""Collectively, the bedtools utilities are a swiss-army knife of`
			`tools for a wide-range of genomics analysis tasks. The most`
			`widely-used tools enable genome arithmetic: that is, set theory`
			`on the genome."""`

			`homepage = "https://github.com/arq5x/bedtools2"`
bedtools2: add v2.30.0 (#24412) 2021-06-19 16:53:21 +08:00			`url = "https://github.com/arq5x/bedtools2/archive/v2.30.0.tar.gz"`
Add package for bedtools2 (#1572) Add package for bedtools2, with support for v2.25.0 and v2.26.0. 2016-09-21 19:23:03 +08:00
bedtools2: add v2.31.0 (#37301) 2023-05-02 11:28:01 +08:00			`version("2.31.0", sha256="183cf9a96aabc50ef4bd557a53fd01557a123c05a0dc87651371878f357439ec")`
bedtools2: add v2.30.0 (#24412) 2021-06-19 16:53:21 +08:00			`version("2.30.0", sha256="c575861ec746322961cd15d8c0b532bb2a19333f1cf167bbff73230a7d67302f")`
Added bedtools2 v2.29.2 and and py-bedtools versions up to v0.8.0 (#19744) 2020-11-30 22:55:49 +08:00			`version("2.29.2", sha256="bc2f36b5d4fc9890c69f607d54da873032628462e88c545dd633d2c787a544a5")`
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("2.27.1", sha256="edcac089d84e63a51f85c3c189469daa7d42180272130b046856faad3cf79112")`
			`version("2.27.0", sha256="e91390b567e577d337c15ca301e264b0355441f5ab90fa4f971622e3043e0ca0")`
			`version("2.26.0", sha256="15db784f60a11b104ccbc9f440282e5780e0522b8d55d359a8318a6b61897977")`
			`version("2.25.0", sha256="159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb")`
			`version("2.23.0", sha256="9dacaa561d11ce9835d1d51e5aeb092bcbe117b7119663ec9a671abac6a36056")`
Add package for bedtools2 (#1572) Add package for bedtools2, with support for v2.25.0 and v2.26.0. 2016-09-21 19:23:03 +08:00
			`depends_on("zlib")`
Bedtools2: add dependencies needed for latest version (#22999) 2021-04-15 17:21:08 +08:00			`depends_on("bzip2", when="@2.29:")`
			`depends_on("xz", when="@2.29:")`
bedtools2: Add missing python build dependency (#18744) (#18746) Makefile invokes python to build some scripts See #18744 2020-09-19 10:38:21 +08:00			`depends_on("python", type="build")`
Add package for bedtools2 (#1572) Add package for bedtools2, with support for v2.25.0 and v2.26.0. 2016-09-21 19:23:03 +08:00
bedtools2: patching to build with gcc@13 (#38254) * bedtools2: patching to build with gcc@13 * bedtools2: patching to build with gcc@13 * Update var/spack/repos/builtin/packages/bedtools2/package.py Yep, sure. Makes sense. Co-authored-by: Alec Scott <alec@bcs.sh> --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Alec Scott <alec@bcs.sh> 2023-06-09 02:59:01 +08:00			`patch("bedtools-gcc13.patch", level=1, when="@2.27:%gcc@13:")`

Add package for bedtools2 (#1572) Add package for bedtools2, with support for v2.25.0 and v2.26.0. 2016-09-21 19:23:03 +08:00			`def install(self, spec, prefix):`
			`make("prefix=%s" % prefix, "install")`