zhangyiss/spack
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
4c254c6c9f
spack/var/spack/repos/builtin/packages/pacbio-daligner/package.py

28 lines
990 B
Python
Raw Normal View History

copyright: update copyright dates for 2020 (#14328)
2019-12-31 14:36:56 +08:00
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers - remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
2018-10-08 04:52:23 +08:00
# Spack Project Developers. See the top-level COPYRIGHT file for details.
adding falcon (#5057) * py-networkx: adding older version py-networkx * py-pypeflow: new package * falcon: adding new package pacbio-daligner: adding new package pacbio-damasker: adding new package pacbio-dazz-db: adding new package pacbio-dextractor: adding new package * py-networkx: modifying version order to be in line with convention * falcon: tweaking py-networkx dependency to satisfy setuptools py-pypeflow: adding missing dependency * pacbio-dextractor: changing hdf5 dependency * pacbio-daligner: adding gmake build dep pacbio-damasker: adding gmake build dep pacbio-dazz-db: adding gmake build dep pacbio-dextractor: adding gmake build dep
2017-08-12 06:26:20 +08:00
#
relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers - remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
2018-10-08 04:52:23 +08:00
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
adding falcon (#5057) * py-networkx: adding older version py-networkx * py-pypeflow: new package * falcon: adding new package pacbio-daligner: adding new package pacbio-damasker: adding new package pacbio-dazz-db: adding new package pacbio-dextractor: adding new package * py-networkx: modifying version order to be in line with convention * falcon: tweaking py-networkx dependency to satisfy setuptools py-pypeflow: adding missing dependency * pacbio-dextractor: changing hdf5 dependency * pacbio-daligner: adding gmake build dep pacbio-damasker: adding gmake build dep pacbio-dazz-db: adding gmake build dep pacbio-dextractor: adding gmake build dep
2017-08-12 06:26:20 +08:00
from spack import *
class PacbioDaligner(MakefilePackage):
"""Daligner: The Dazzler "Overlap" Module. This is a special fork
required for some pacbio utilities."""
homepage = "https://github.com/PacificBiosciences/DALIGNER"
Add top-level attributes for git M-P packages
2018-07-24 09:55:17 +08:00
git = "https://github.com/PacificBiosciences/DALIGNER.git"
adding falcon (#5057) * py-networkx: adding older version py-networkx * py-pypeflow: new package * falcon: adding new package pacbio-daligner: adding new package pacbio-damasker: adding new package pacbio-dazz-db: adding new package pacbio-dextractor: adding new package * py-networkx: modifying version order to be in line with convention * falcon: tweaking py-networkx dependency to satisfy setuptools py-pypeflow: adding missing dependency * pacbio-dextractor: changing hdf5 dependency * pacbio-daligner: adding gmake build dep pacbio-damasker: adding gmake build dep pacbio-dazz-db: adding gmake build dep pacbio-dextractor: adding gmake build dep
2017-08-12 06:26:20 +08:00
Add top-level attributes for git M-P packages
2018-07-24 09:55:17 +08:00
version('2017-08-05', commit='0fe5240d2cc6b55bf9e04465b700b76110749c9d')
adding falcon (#5057) * py-networkx: adding older version py-networkx * py-pypeflow: new package * falcon: adding new package pacbio-daligner: adding new package pacbio-damasker: adding new package pacbio-dazz-db: adding new package pacbio-dextractor: adding new package * py-networkx: modifying version order to be in line with convention * falcon: tweaking py-networkx dependency to satisfy setuptools py-pypeflow: adding missing dependency * pacbio-dextractor: changing hdf5 dependency * pacbio-daligner: adding gmake build dep pacbio-damasker: adding gmake build dep pacbio-dazz-db: adding gmake build dep pacbio-dextractor: adding gmake build dep
2017-08-12 06:26:20 +08:00
depends_on('gmake', type='build')
depends_on('pacbio-dazz-db')
def edit(self, spec, prefix):
mkdir(prefix.bin)
makefile = FileFilter('Makefile')
flake8: fix flake8 issues with invalid escapes - in many files, regular strings were used in places where raw strings should've been used. - convert these to raw strings and get rid of new flake8 errors
2019-01-01 15:25:40 +08:00
makefile.filter(r'DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
adding falcon (#5057) * py-networkx: adding older version py-networkx * py-pypeflow: new package * falcon: adding new package pacbio-daligner: adding new package pacbio-damasker: adding new package pacbio-dazz-db: adding new package pacbio-dextractor: adding new package * py-networkx: modifying version order to be in line with convention * falcon: tweaking py-networkx dependency to satisfy setuptools py-pypeflow: adding missing dependency * pacbio-dextractor: changing hdf5 dependency * pacbio-daligner: adding gmake build dep pacbio-damasker: adding gmake build dep pacbio-dazz-db: adding gmake build dep pacbio-dextractor: adding gmake build dep
2017-08-12 06:26:20 +08:00
gmf = FileFilter('GNUmakefile')
flake8: fix flake8 issues with invalid escapes - in many files, regular strings were used in places where raw strings should've been used. - convert these to raw strings and get rid of new flake8 errors
2019-01-01 15:25:40 +08:00
gmf.filter(r'rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
adding falcon (#5057) * py-networkx: adding older version py-networkx * py-pypeflow: new package * falcon: adding new package pacbio-daligner: adding new package pacbio-damasker: adding new package pacbio-dazz-db: adding new package pacbio-dextractor: adding new package * py-networkx: modifying version order to be in line with convention * falcon: tweaking py-networkx dependency to satisfy setuptools py-pypeflow: adding missing dependency * pacbio-dextractor: changing hdf5 dependency * pacbio-daligner: adding gmake build dep pacbio-damasker: adding gmake build dep pacbio-dazz-db: adding gmake build dep pacbio-dextractor: adding gmake build dep
2017-08-12 06:26:20 +08:00
'cp ${ALL} ' + prefix.bin)
Reference in New Issue Copy Permalink