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| author | Desmond Orton <odesmond21@gmail.com> | 2021-06-03 18:58:08 -0500 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2021-06-03 23:58:08 +0000 |
| commit | a85bc4eee13fb9a8d3abc48635775b925e5f2f13 (patch) | |
| tree | 87027ff0397ec9d54e776491c3badf63a3e46f01 /var | |
| parent | 9903d05be9ebd1fee1bb69b4204bbb044307c648 (diff) | |
| download | spack-a85bc4eee13fb9a8d3abc48635775b925e5f2f13.tar.gz spack-a85bc4eee13fb9a8d3abc48635775b925e5f2f13.tar.bz2 spack-a85bc4eee13fb9a8d3abc48635775b925e5f2f13.tar.xz spack-a85bc4eee13fb9a8d3abc48635775b925e5f2f13.zip | |
New package: py-haphpipe (#23769)
* New Package:py-haphpipe@1.0.3
* removed llvm restrict. & changed freebayes
* Style fix
* Removed pip, wheel, added url for deps list
* used proper gsutil naming
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* url src for deps, samtools fix
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/py-haphpipe/package.py | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/py-haphpipe/package.py b/var/spack/repos/builtin/packages/py-haphpipe/package.py new file mode 100644 index 0000000000..191ad706a8 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-haphpipe/package.py @@ -0,0 +1,49 @@ +# Copyright 2013-2021 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 PyHaphpipe(PythonPackage): + """HAplotype and PHylodynamics pipeline for viral assembly, + population genetics, and phylodynamics.""" + + homepage = "https://github.com/gwcbi/haphpipe" + url = "https://github.com/gwcbi/haphpipe/archive/v1.0.3.tar.gz" + + maintainers = ['dorton21'] + + version('1.0.3', sha256='9a9e8632a217ff4207c1dea66887a471e0ea04bbb7c0f0d72631acaba214bd37') + + # Deps. taken from + # https://github.com/bioconda/bioconda-recipes/blob/master/recipes/haphpipe/meta.yaml + # http://bioconda.github.io/recipes/haphpipe/README.html + # https://github.com/gwcbi/haphpipe/blob/master/environment.yml + depends_on('python@3.7:', type=('build', 'run')) + depends_on('py-future', type=('build', 'run')) + depends_on('py-pyyaml', type=('build', 'run')) + depends_on('py-biopython@1.73:', type=('build', 'run')) + depends_on('py-gsutil', type=('build', 'run')) + depends_on('py-sierrapy', type=('build', 'run')) + depends_on('py-setuptools', type='build') + + depends_on('bowtie2', type=('build', 'run')) + depends_on('blast-plus', type=('build', 'run')) + depends_on('freebayes', type=('build', 'run')) + depends_on('modeltest-ng', type=('build', 'run')) + depends_on('libdeflate', type=('build', 'run')) + depends_on('sratoolkit', type=('build', 'run')) + depends_on('spades', type=('build', 'run')) + depends_on('seqtk', type=('build', 'run')) + depends_on('raxml-ng~mpi', type=('build', 'run')) + depends_on('gatk@3.8-0', type=('build', 'run')) + depends_on('trinity', type=('build', 'run')) + depends_on('trimmomatic@0.38:', type=('build', 'run')) + depends_on('flash@1.2.11:', type=('build', 'run')) + depends_on('mummer@3.23:', type=('build', 'run')) + depends_on('bwa', type=('build', 'run')) + depends_on('samtools@1.9:', type=('build', 'run')) + depends_on('mafft', type=('build', 'run')) + depends_on('picard', type=('build', 'run')) |