diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/repeatmasker/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/repeatmasker/package.py | 84 |
1 files changed, 37 insertions, 47 deletions
diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py index 47d267967f..d55fd69bbc 100644 --- a/var/spack/repos/builtin/packages/repeatmasker/package.py +++ b/var/spack/repos/builtin/packages/repeatmasker/package.py @@ -10,36 +10,34 @@ from spack.package import * class Repeatmasker(Package): """RepeatMasker is a program that screens DNA sequences for interspersed - repeats and low complexity DNA sequences.""" + repeats and low complexity DNA sequences.""" homepage = "https://www.repeatmasker.org" - version('4.1.2-p1', sha256='4be54bf6c050422b211e24a797feb06fd7954c8b4ee6f3ece94cb6faaf6b0e96') - version('4.0.9', sha256='8d67415d89ed301670b7632ea411f794c6e30d8ed0f007a726c4b0a39c8638e5') - version('4.0.7', sha256='16faf40e5e2f521146f6692f09561ebef5f6a022feb17031f2ddb3e3aabcf166') + version("4.1.2-p1", sha256="4be54bf6c050422b211e24a797feb06fd7954c8b4ee6f3ece94cb6faaf6b0e96") + version("4.0.9", sha256="8d67415d89ed301670b7632ea411f794c6e30d8ed0f007a726c4b0a39c8638e5") + version("4.0.7", sha256="16faf40e5e2f521146f6692f09561ebef5f6a022feb17031f2ddb3e3aabcf166") - variant('crossmatch', description='Enable CrossMatch search engine', - default=False) + variant("crossmatch", description="Enable CrossMatch search engine", default=False) - depends_on('perl', type=('build', 'run')) - depends_on('perl-text-soundex', type=('build', 'run')) - 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("perl", type=("build", "run")) + depends_on("perl-text-soundex", type=("build", "run")) + 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') + depends_on("phrap-crossmatch-swat", type=("build", "run"), when="+crossmatch") - patch('utf8.patch', when='@:4.0') + patch("utf8.patch", when="@:4.0") def url_for_version(self, version): - if version >= Version('4.1.0'): - url = 'http://www.repeatmasker.org/RepeatMasker/RepeatMasker-{0}.tar.gz' + 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' + url = "http://www.repeatmasker.org/RepeatMasker/RepeatMasker-open-{0}.tar.gz" return url.format(version.dashed) def install(self, spec, prefix): @@ -62,50 +60,42 @@ class Repeatmasker(Package): config_answers = [] - if spec.satisfies('@:4.0.7'): + if spec.satisfies("@:4.0.7"): # 4.0.9 removes a bunch of the interactive options - config_answers.extend(['', - self.spec['perl'].command.path, - self.stage.source_path]) + config_answers.extend(["", self.spec["perl"].command.path, self.stage.source_path]) # set path to trf - config_answers.append(self.spec['trf'].prefix.bin.trf) + config_answers.append(self.spec["trf"].prefix.bin.trf) # add crossmatch search - if '+crossmatch' in spec: - crossmatch = self.spec['phrap-crossmatch-swat'].prefix.bin - config_answers.extend(['1', crossmatch, 'N']) + if "+crossmatch" in spec: + crossmatch = self.spec["phrap-crossmatch-swat"].prefix.bin + config_answers.extend(["1", crossmatch, "N"]) # set default BLAST search - config_answers.extend(['2', - self.spec['ncbi-rmblastn'].prefix.bin, - 'Y']) + config_answers.extend(["2", self.spec["ncbi-rmblastn"].prefix.bin, "Y"]) # set non-default HMMER search - if spec.satisfies('@4.0.9:'): - config_answers.extend(['3', - self.spec['hmmer'].prefix.bin, - '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']) + config_answers.extend(["4", self.spec["hmmer"].prefix.bin, "N"]) # end configuration - config_answers.append('5') + config_answers.append("5") - config_answers_filename = 'spack-config.in' + config_answers_filename = "spack-config.in" - with open(config_answers_filename, 'w') as f: - f.write('\n'.join(config_answers)) + with open(config_answers_filename, "w") as f: + f.write("\n".join(config_answers)) - with open(config_answers_filename, 'r') as f: - perl = which('perl') - perl('configure', input=f) + with open(config_answers_filename, "r") as f: + perl = which("perl") + perl("configure", input=f) # fix perl paths # every sbang points to perl, so a regex will suffice - for f in glob.glob('*.pm'): - filter_file('#!.*', '#!%s' % spec['perl'].command, f) + for f in glob.glob("*.pm"): + filter_file("#!.*", "#!%s" % spec["perl"].command, f) - install_tree('.', prefix.bin) + install_tree(".", prefix.bin) |