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repeatmasker: update and fix package (#22785)

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- version 4.0.7 was not building
- version 4.0.9 was not setting search correctly due to an extra "return"
  in config
- added version 4.1.2-p1
- new version needs py-h5py
- new version does not need utf8 patch
- url format changed
This commit is contained in:
Glenn Johnson 2021-04-06 01:35:51 -05:00 committed by GitHub
parent a4f19853b8
commit 6df1b509fa
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GPG key ID: 4AEE18F83AFDEB23
1 changed files with 23 additions and 12 deletions
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35
var/spack/repos/builtin/packages/repeatmasker/package.py
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@ -12,8 +12,8 @@ class Repeatmasker(Package):
repeats and low complexity DNA sequences."""
homepage = "http://www.repeatmasker.org"
url = "http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz"
version('4.1.2-p1', sha256='4be54bf6c050422b211e24a797feb06fd7954c8b4ee6f3ece94cb6faaf6b0e96')
version('4.0.9', sha256='8d67415d89ed301670b7632ea411f794c6e30d8ed0f007a726c4b0a39c8638e5')
version('4.0.7', sha256='16faf40e5e2f521146f6692f09561ebef5f6a022feb17031f2ddb3e3aabcf166')
@ -25,15 +25,21 @@ class Repeatmasker(Package):
depends_on('hmmer')
depends_on('ncbi-rmblastn')
depends_on('trf')
depends_on('python', when='@4.1:', type=('build', 'run'))
depends_on('py-h5py', when='@4.1:', type=('build', 'run'))
depends_on('phrap-crossmatch-swat', type=('build', 'run'),
when='+crossmatch')
patch('utf8.patch')
patch('utf8.patch', when='@:4.0')
def url_for_version(self, version):
url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz'
return url.format(version.dashed)
if version >= Version('4.1.0'):
url = 'http://www.repeatmasker.org/RepeatMasker/RepeatMasker-{0}.tar.gz'
return url.format(version)
else:
url = 'http://www.repeatmasker.org/RepeatMasker/RepeatMasker-open-{0}.tar.gz'
return url.format(version.dashed)
def install(self, spec, prefix):
# Config questions consist of:
@ -55,14 +61,14 @@ def install(self, spec, prefix):
config_answers = []
if spec.satisfies('@4.0.9:'):
if spec.satisfies('@:4.0.7'):
# 4.0.9 removes a bunch of the interactive options
config_answers.append('')
else:
config_answers.extend(['',
self.spec['perl'].command.path,
self.stage.source_path,
self.spec['trf'].prefix.bin.trf])
self.stage.source_path])
# set path to trf
config_answers.append(self.spec['trf'].prefix.bin.trf)
# add crossmatch search
if '+crossmatch' in spec:
@ -75,9 +81,14 @@ def install(self, spec, prefix):
'Y'])
# set non-default HMMER search
config_answers.extend(['3',
self.spec['hmmer'].prefix,
'N'])
if spec.satisfies('@4.0.9:'):
config_answers.extend(['3',
self.spec['hmmer'].prefix.bin,
'N'])
else:
config_answers.extend(['4',
self.spec['hmmer'].prefix.bin,
'N'])
# end configuration
config_answers.append('5')