b932c14008
* Bump the package API of the `builtin` repo to `v2.0`
* Move `var/spack/repos/builtin` -> `var/spack/repos/spack_repo/builtin`
* Move test repos `var/spack/repos/{builtin.mock,tutorial,...}` -> `var/spack/test_repos/`
* Update package dir names to v2 format (`-` -> `_` etc)
* Change absolute imports `from spack.pkg.builtin.my_pkg ...` to relative imports `from ..my_pkg.package ...`
Users who have a repo on top of builtin should change imports from
```python
from spack.pkg.builtin.my_pkg import MyPkg
```
to
```python
from spack_repo.builtin.packages.my_pkg.package import MyPkg
```
and can configure their editors with
```
PYTHONPATH=$spack/lib/spack:$spack/var/spack/repos
```
[skip-verify-checksums]
60 lines
2.4 KiB
Python
60 lines
2.4 KiB
Python
# Copyright Spack Project Developers. See COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Busco(PythonPackage):
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"""Assesses genome assembly and annotation completeness with Benchmarking
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Universal Single-Copy Orthologs"""
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homepage = "https://busco.ezlab.org/"
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url = "https://gitlab.com/api/v4/projects/ezlab%2Fbusco/repository/archive.tar.gz?sha=2.0.1"
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git = "https://gitlab.com/ezlab/busco.git"
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maintainers("snehring")
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license("MIT")
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version("5.4.3", sha256="8b92dcc32691f7c1629aaaa7bd54f96073273ba7de5a3a8586fe552c51a9d36a")
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version("4.1.3", sha256="08ded26aeb4f6aef791cd88524c3c00792a054c7672ea05219f468d495e7b072")
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# TODO: check the installation procedure for version 3.0.2
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# and uncomment the following line
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# version('3.0.2', sha256='dbea093315b766b0f7c4fe3cafbbdf51ade79ec84bde04f1f437b48333200f34')
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# There is no tag for version 3.0.1
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version("3.0.1", commit="078252e00399550d7b0e8941cd4d986c8e868a83")
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version("2.0.1", sha256="bd72a79b880370e9b61b8c722e171818c7c85d46cc1e2f80595df2738a7e220c")
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# https://busco.ezlab.org/busco_userguide.html#manual-installation
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depends_on("python@3.3:", when="@4:", type=("build", "run"))
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# pip silently replaces distutils with setuptools
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depends_on("py-setuptools", when="@3:", type="build")
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depends_on("blast-plus")
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depends_on("hmmer")
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depends_on("augustus")
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depends_on("py-biopython", when="@4.1.3:", type=("build", "run"))
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depends_on("py-pandas", when="@5:", type="run")
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depends_on("bbmap", when="@5:", type="run")
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depends_on("prodigal", when="@5:", type="run")
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depends_on("metaeuk", when="@5:", type="run")
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depends_on("sepp", when="@5:", type="run")
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def install(self, spec, prefix):
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if self.spec.satisfies("@4.1.3:"):
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install_tree("bin", prefix.bin)
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install_tree("config", prefix.config)
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super().install(spec, prefix)
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if self.spec.satisfies("@3.0.1"):
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with working_dir("scripts"):
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mkdirp(prefix.bin)
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install("generate_plot.py", prefix.bin)
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install("run_BUSCO.py", prefix.bin)
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install_tree("config", prefix.config)
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super().install(spec, prefix)
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if self.spec.satisfies("@2.0.1"):
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mkdirp(prefix.bin)
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install("BUSCO.py", prefix.bin)
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install("BUSCO_plot.py", prefix.bin)
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