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Add py-pipits 2.4 (#12074)

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* Add py-pipits 2.4

* Flake8 fix
This commit is contained in:
Adam J. Stewart 2019-07-30 17:10:57 -05:00 committed by GitHub
parent 175abecc0b
commit e13bc0212c
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GPG Key ID: 4AEE18F83AFDEB23
4 changed files with 81 additions and 8 deletions
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26
var/spack/repos/builtin/packages/py-pipits/package.py
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@ -10,19 +10,29 @@ class PyPipits(PythonPackage):
"""Automated pipeline for analyses of fungal ITS from the Illumina"""
homepage = "https://github.com/hsgweon/pipits"
url = "https://github.com/hsgweon/pipits/archive/1.5.0.tar.gz"
url = "https://github.com/hsgweon/pipits/archive/2.4.tar.gz"
version('2.4', sha256='b08a9d70ac6e5dd1c64d56b77384afd69e21e7d641b2fc4416feff862a2cd054')
version('1.5.0', '3f9b52bd7ffbcdb96d7bec150275070a')
depends_on('python@:2.999', type=('build', 'run'))
# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pipits/meta.yaml
depends_on('python@3:', type=('build', 'run'), when='@2:')
depends_on('python@:2', type=('build', 'run'), when='@:1')
depends_on('py-setuptools', type='build', when='@2:')
depends_on('py-pispino@1.1:', type=('build', 'run'), when='@2:')
depends_on('vsearch', type='run')
depends_on('fastx-toolkit', type='run')
depends_on('hmmer', type='run')
depends_on('itsx', type='run')
depends_on('py-biom-format', type=('build', 'run'))
depends_on('rdptools', type='run', when='@2:')
depends_on('py-numpy', type=('build', 'run'))
depends_on('java', type=('build', 'run'))
depends_on('hmmer')
depends_on('fastx-toolkit')
depends_on('vsearch')
depends_on('itsx')
depends_on('rdp-classifier')
depends_on('py-pandas', type=('build', 'run'), when='@2:')
depends_on('py-progressbar2', type=('build', 'run'), when='@2:')
depends_on('py-requests', type=('build', 'run'), when='@2:')
depends_on('seqkit', type='run')
depends_on('java', type=('build', 'run'), when='@:1')
depends_on('rdp-classifier', type='run', when='@:1')
resource(
name='UNITE_retrained',

20
var/spack/repos/builtin/packages/py-pispino/package.py Normal file
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@ -0,0 +1,20 @@
# Copyright 2013-2019 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 import *
class PyPispino(PythonPackage):
"""PISPINO (PIpits SPIN-Off tools)."""
homepage = "https://github.com/hsgweon/pispino"
url = "https://github.com/hsgweon/pispino/archive/1.1.tar.gz"
version('1.1', sha256='8fb2e1c0ae38ecca7c637de9c0b655eb18fc67d7838ceb5a6902555ea12416c0')
# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pispino/meta.yaml
depends_on('py-setuptools', type='build')
depends_on('vsearch', type='run')
depends_on('fastx-toolkit', type='run')

23
var/spack/repos/builtin/packages/rdptools/package.py Normal file
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@ -0,0 +1,23 @@
# Copyright 2013-2019 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 import *
class Rdptools(MakefilePackage):
"""Collection of commonly used RDP Tools for easy building."""
homepage = "https://github.com/rdpstaff/RDPTools"
url = "https://github.com/rdpstaff/RDPTools/archive/2.0.2.tar.gz"
version('2.0.2', sha256='fc3d7f8129b45e602fc2c23e5e037a7f48c14d5a6b05c64f8c1d48e9767ac01d')
# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/rdptools/meta.yaml
depends_on('java')
depends_on('ant')
depends_on('python')
def install(self, spec, prefix):
install_tree('.', prefix)

20
var/spack/repos/builtin/packages/seqkit/package.py Normal file
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@ -0,0 +1,20 @@
# Copyright 2013-2019 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 import *
class Seqkit(Package):
"""A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
in Golang."""
homepage = "http://bioinf.shenwei.me/seqkit"
url = "https://github.com/shenwei356/seqkit/releases/download/v0.10.1/seqkit_linux_amd64.tar.gz"
version('0.10.1', sha256='82f1c86dc4bd196403a56c2bf3ec063e5674a71777e68d940c4cc3d8411d2e9d')
def install(self, spec, prefix):
mkdir(prefix.bin)
install('seqkit', prefix.bin)