From e13bc0212c51ac6894fa5139b70c953f09b9f833 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 30 Jul 2019 17:10:57 -0500 Subject: Add py-pipits 2.4 (#12074) * Add py-pipits 2.4 * Flake8 fix --- .../repos/builtin/packages/py-pipits/package.py | 26 +++++++++++++++------- .../repos/builtin/packages/py-pispino/package.py | 20 +++++++++++++++++ .../repos/builtin/packages/rdptools/package.py | 23 +++++++++++++++++++ var/spack/repos/builtin/packages/seqkit/package.py | 20 +++++++++++++++++ 4 files changed, 81 insertions(+), 8 deletions(-) create mode 100644 var/spack/repos/builtin/packages/py-pispino/package.py create mode 100644 var/spack/repos/builtin/packages/rdptools/package.py create mode 100644 var/spack/repos/builtin/packages/seqkit/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-pipits/package.py b/var/spack/repos/builtin/packages/py-pipits/package.py index ac88278d20..b97ef7b61b 100644 --- a/var/spack/repos/builtin/packages/py-pipits/package.py +++ b/var/spack/repos/builtin/packages/py-pipits/package.py @@ -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', diff --git a/var/spack/repos/builtin/packages/py-pispino/package.py b/var/spack/repos/builtin/packages/py-pispino/package.py new file mode 100644 index 0000000000..bcb3c04e38 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pispino/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/rdptools/package.py b/var/spack/repos/builtin/packages/rdptools/package.py new file mode 100644 index 0000000000..22644f6606 --- /dev/null +++ b/var/spack/repos/builtin/packages/rdptools/package.py @@ -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) diff --git a/var/spack/repos/builtin/packages/seqkit/package.py b/var/spack/repos/builtin/packages/seqkit/package.py new file mode 100644 index 0000000000..2a58be05b6 --- /dev/null +++ b/var/spack/repos/builtin/packages/seqkit/package.py @@ -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) -- cgit v1.2.3-70-g09d2