62927654dd
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
43 lines
1.6 KiB
Python
43 lines
1.6 KiB
Python
# 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 *
|
|
import glob
|
|
import os
|
|
|
|
|
|
class Hybpiper(Package):
|
|
"""HybPiper was designed for targeted sequence capture, in which DNA
|
|
sequencing libraries are enriched for gene regions of interest,
|
|
especially for phylogenetics. HybPiper is a suite of Python scripts
|
|
that wrap and connect bioinformatics tools in order to extract target
|
|
sequences from high-throughput DNA sequencing reads"""
|
|
|
|
homepage = "https://github.com/mossmatters/HybPiper"
|
|
url = "https://github.com/mossmatters/HybPiper/archive/v1.2.0.tar.gz"
|
|
git = "https://github.com/mossmatters/HybPiper/HybPiper.git"
|
|
|
|
version('1.3.1', sha256='7ca07a9390d1ca52c72721774fa220546f18d3fa3b58500f68f3b2d89dbc0ecf')
|
|
version('1.2.0', sha256='34c7b324e9bcacb6ccfe87dc50615d6f93866433b61a59291707efa858b6df57')
|
|
|
|
depends_on('python@2.7:', type=('build', 'run'))
|
|
depends_on('py-biopython', type=('build', 'run'))
|
|
depends_on('exonerate')
|
|
depends_on('blast-plus')
|
|
depends_on('spades')
|
|
depends_on('parallel')
|
|
depends_on('bwa')
|
|
depends_on('samtools')
|
|
|
|
def setup_envionment(self, spack_env, run_env):
|
|
run_env.set('HYBPIPER_HOME', prefix)
|
|
|
|
def install(self, spec, prefix):
|
|
mkdirp(prefix.bin)
|
|
files = glob.iglob("*.py")
|
|
for file in files:
|
|
if os.path.isfile(file):
|
|
install(file, prefix.bin)
|