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redundans: add 0.14a (#10006)

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Also update install to use globbing
This commit is contained in:
Justin Stanley 2019-01-30 18:55:59 -06:00 committed by Peter Scheibel
parent 9bfcbcc155
commit 993745b919
1 changed files with 15 additions and 10 deletions
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25
var/spack/repos/builtin/packages/redundans/package.py
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@ -4,6 +4,7 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT) # SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import * from spack import *
import glob
class Redundans(Package): class Redundans(Package):
@ -11,7 +12,9 @@ class Redundans(Package):
homepage = "https://github.com/Gabaldonlab/redundans" homepage = "https://github.com/Gabaldonlab/redundans"
url = "https://github.com/Gabaldonlab/redundans/archive/v0.13c.tar.gz" url = "https://github.com/Gabaldonlab/redundans/archive/v0.13c.tar.gz"
git = "https://github.com/Gabaldonlab/redundans.git"
version('0.14a', commit='a20215a862aed161cbfc79df9133206156a1e9f0')
version('0.13c', '2003fb7c70521f5e430553686fd1a594') version('0.13c', '2003fb7c70521f5e430553686fd1a594')
depends_on('python', type=('build', 'run')) depends_on('python', type=('build', 'run'))
@ -29,16 +32,18 @@ class Redundans(Package):
def install(self, spec, prefix): def install(self, spec, prefix):
sspace_location = join_path(spec['sspace-standard'].prefix, sspace_location = join_path(spec['sspace-standard'].prefix,
'SSPACE_Standard_v3.0.pl') 'SSPACE_Standard_v3.0.pl')
mkdirp(prefix.bin)
filter_file(r'sspacebin = os.path.join(.*)$', filter_file(r'sspacebin = os.path.join(.*)$',
'sspacebin = \'' + sspace_location + '\'', 'sspacebin = \'' + sspace_location + '\'',
'redundans.py') 'redundans.py')
install('redundans.py', prefix.bin)
with working_dir('bin'): binfiles = ['redundans.py', 'bin/filterReads.py']
install('fasta2homozygous.py', prefix.bin) binfiles.extend(glob.glob('bin/fast?2*.py'))
install('fasta2split.py', prefix.bin)
install('fastq2insert_size.py', prefix.bin) # new internal dep with 0.14a
install('fastq2mates.py', prefix.bin) if spec.satisfies('@0.14a:'):
install('fastq2shuffled.py', prefix.bin) binfiles.append('bin/denovo.py')
install('fastq2sspace.py', prefix.bin)
install('filterReads.py', prefix.bin) mkdirp(prefix.bin)
for f in binfiles:
install(f, prefix.bin)