diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/reditools/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/reditools/package.py | 95 |
1 files changed, 49 insertions, 46 deletions
diff --git a/var/spack/repos/builtin/packages/reditools/package.py b/var/spack/repos/builtin/packages/reditools/package.py index 45c2fb82ae..1033e2bdea 100644 --- a/var/spack/repos/builtin/packages/reditools/package.py +++ b/var/spack/repos/builtin/packages/reditools/package.py @@ -17,69 +17,72 @@ class Reditools(PythonPackage): in the standard BAM format and implement a variety of filters.""" homepage = "https://github.com/BioinfoUNIBA/REDItools" - git = "https://github.com/BioinfoUNIBA/REDItools.git" + git = "https://github.com/BioinfoUNIBA/REDItools.git" - maintainers = ['glennpj'] + maintainers = ["glennpj"] - version('1.3_2020-08-03', commit='2dc71277a25e667797c363d1fca22726249774a3') - version('1.3_2020-03-20', commit='cf47f3d54f324aeb9650bcf8bfacf5a967762a55') + version("1.3_2020-08-03", commit="2dc71277a25e667797c363d1fca22726249774a3") + version("1.3_2020-03-20", commit="cf47f3d54f324aeb9650bcf8bfacf5a967762a55") - variant('nature_protocol', default=False, - description='Install the Nature Protocol scripts and files') + variant( + "nature_protocol", + default=False, + description="Install the Nature Protocol scripts and files", + ) # pip silently replaces distutils with setuptools - depends_on('py-setuptools', type='build') - depends_on('py-reindent', type='build', when='^python@3:') - depends_on('blat', type='run') - depends_on('py-fisher', type='run') - depends_on('py-numpy', type='run') - depends_on('py-pandas', type='run') - depends_on('py-pysam', type='run') - depends_on('py-scipy', type='run') - depends_on('tabix', type='run') + depends_on("py-setuptools", type="build") + depends_on("py-reindent", type="build", when="^python@3:") + depends_on("blat", type="run") + depends_on("py-fisher", type="run") + depends_on("py-numpy", type="run") + depends_on("py-pandas", type="run") + depends_on("py-pysam", type="run") + depends_on("py-scipy", type="run") + depends_on("tabix", type="run") # Nature Protocol - depends_on('bcftools', type='run', when='+nature_protocol') - depends_on('bedtools2', type='run', when='+nature_protocol') - depends_on('bwa', type='run', when='+nature_protocol') - depends_on('bzip2', type='run', when='+nature_protocol') - depends_on('fastp', type='run', when='+nature_protocol') - depends_on('fastqc', type='run', when='+nature_protocol') - depends_on('git', type='run', when='+nature_protocol') - depends_on('gmap-gsnap', type='run', when='+nature_protocol') - depends_on('htslib', type='run', when='+nature_protocol') - depends_on('libdeflate', type='run', when='+nature_protocol') - depends_on('py-bx-python', type='run', when='+nature_protocol') - depends_on('py-rseqc', type='run', when='+nature_protocol') - depends_on('samtools', type='run', when='+nature_protocol') - depends_on('star', type='run', when='+nature_protocol') - depends_on('wget', type='run', when='+nature_protocol') + depends_on("bcftools", type="run", when="+nature_protocol") + depends_on("bedtools2", type="run", when="+nature_protocol") + depends_on("bwa", type="run", when="+nature_protocol") + depends_on("bzip2", type="run", when="+nature_protocol") + depends_on("fastp", type="run", when="+nature_protocol") + depends_on("fastqc", type="run", when="+nature_protocol") + depends_on("git", type="run", when="+nature_protocol") + depends_on("gmap-gsnap", type="run", when="+nature_protocol") + depends_on("htslib", type="run", when="+nature_protocol") + depends_on("libdeflate", type="run", when="+nature_protocol") + depends_on("py-bx-python", type="run", when="+nature_protocol") + depends_on("py-rseqc", type="run", when="+nature_protocol") + depends_on("samtools", type="run", when="+nature_protocol") + depends_on("star", type="run", when="+nature_protocol") + depends_on("wget", type="run", when="+nature_protocol") - patch('interpreter.patch') - patch('setup.py.patch') - patch('batch_sort.patch', when='^python@3:') + patch("interpreter.patch") + patch("setup.py.patch") + patch("batch_sort.patch", when="^python@3:") - @run_before('install') + @run_before("install") def p2_to_p3(self): - if '^python@3:' in self.spec: + if "^python@3:" in self.spec: # clean up space/tab mixing - reindent = which('reindent') - reindent('--nobackup', '--recurse', '.') + reindent = which("reindent") + reindent("--nobackup", "--recurse", ".") # convert to be python3 compatible - p2_to_p3 = which('2to3') - p2_to_p3('--nobackups', '--write', '.') + p2_to_p3 = which("2to3") + p2_to_p3("--nobackups", "--write", ".") - @run_after('install') + @run_after("install") def nature_protocol(self): - if '+nature_protocol' in self.spec: + if "+nature_protocol" in self.spec: mkdirp(prefix.NPfiles) - install_tree('NPfiles', prefix.NPfiles) + install_tree("NPfiles", prefix.NPfiles) ignore_files = [ - 'conda_pckg_installer_docker.py', - 'conda_pckgs_installer.py', - 'download-prepare-data-NP_docker.py', + "conda_pckg_installer_docker.py", + "conda_pckgs_installer.py", + "download-prepare-data-NP_docker.py", ] docker_conda = lambda p: p in ignore_files - install_tree('NPscripts', prefix.bin, ignore=docker_conda) + install_tree("NPscripts", prefix.bin, ignore=docker_conda) |