diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/ea-utils/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/ea-utils/package.py | 45 |
1 files changed, 23 insertions, 22 deletions
diff --git a/var/spack/repos/builtin/packages/ea-utils/package.py b/var/spack/repos/builtin/packages/ea-utils/package.py index 4a9bbd1365..edfa362492 100644 --- a/var/spack/repos/builtin/packages/ea-utils/package.py +++ b/var/spack/repos/builtin/packages/ea-utils/package.py @@ -10,45 +10,46 @@ from spack.package import * class EaUtils(MakefilePackage): """Command-line tools for processing biological sequencing data. Barcode - demultiplexing, adapter trimming, etc. Primarily written to support an - Illumina based pipeline - but should work with any FASTQs.""" + demultiplexing, adapter trimming, etc. Primarily written to support an + Illumina based pipeline - but should work with any FASTQs.""" homepage = "https://expressionanalysis.github.io/ea-utils/" url = "https://github.com/ExpressionAnalysis/ea-utils/archive/1.04.807.tar.gz" git = "https://github.com/ExpressionAnalysis/ea-utils.git" - maintainers = ['snehring'] + maintainers = ["snehring"] - version('2021-10-20', commit='10c21926a4dce4289d5052acfd73b8e744d4fede') - version('1.04.807', sha256='aa09d25e6aa7ae71d2ce4198a98e58d563f151f8ff248e4602fa437f12b8d05f', - deprecated=True) + version("2021-10-20", commit="10c21926a4dce4289d5052acfd73b8e744d4fede") + version( + "1.04.807", + sha256="aa09d25e6aa7ae71d2ce4198a98e58d563f151f8ff248e4602fa437f12b8d05f", + deprecated=True, + ) - depends_on('sparsehash') - depends_on('zlib') - depends_on('gsl') - depends_on('bamtools') - depends_on('perl', type=['build', 'run']) + depends_on("sparsehash") + depends_on("zlib") + depends_on("gsl") + depends_on("bamtools") + depends_on("perl", type=["build", "run"]) - build_directory = 'clipper' + build_directory = "clipper" def edit(self, spec, prefix): with working_dir(self.build_directory): - filter_file('/usr', prefix, 'Makefile') + filter_file("/usr", prefix, "Makefile") # remove tests from all rule - filter_file(r'^all:.*$', 'all: $(BIN)', 'Makefile') + filter_file(r"^all:.*$", "all: $(BIN)", "Makefile") # remove the vendored sparsehash - filter_file(' sparsehash', '', 'Makefile') + filter_file(" sparsehash", "", "Makefile") # replace system perl references for f in next(os.walk(os.getcwd()))[2]: - filter_file('/usr/bin/perl', spec['perl'].prefix.bin.perl, f) + filter_file("/usr/bin/perl", spec["perl"].prefix.bin.perl, f) # fix up test script require path - tests = ['join.t', 'mcf.t', 'multx.t'] - rep = 'require "{0}";'.format(os.path.join(os.getcwd(), - 't', 'test-prep.pl')) + tests = ["join.t", "mcf.t", "multx.t"] + rep = 'require "{0}";'.format(os.path.join(os.getcwd(), "t", "test-prep.pl")) for f in tests: - filter_file(r'^require.*$', rep, os.path.join(os.getcwd(), - 't', f)) + filter_file(r"^require.*$", rep, os.path.join(os.getcwd(), "t", f)) def flag_handler(self, name, flags): - if name.lower() == 'cxxflags': + if name.lower() == "cxxflags": flags.append(self.compiler.cxx11_flag) return (flags, None, None) |