diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/scalpel/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/scalpel/package.py | 71 |
1 files changed, 42 insertions, 29 deletions
diff --git a/var/spack/repos/builtin/packages/scalpel/package.py b/var/spack/repos/builtin/packages/scalpel/package.py index 31b91f0249..e81a2592b5 100644 --- a/var/spack/repos/builtin/packages/scalpel/package.py +++ b/var/spack/repos/builtin/packages/scalpel/package.py @@ -8,36 +8,40 @@ from spack.package import * class Scalpel(MakefilePackage, SourceforgePackage): """Scalpel is a software package for detecting INDELs (INsertions and - DELetions) mutations in a reference genome which has been sequenced - with next-generation sequencing technology. + DELetions) mutations in a reference genome which has been sequenced + with next-generation sequencing technology. """ homepage = "http://scalpel.sourceforge.net/index.html" sourceforge_mirror_path = "scalpel/scalpel-0.5.4.tar.gz" - version('0.5.4', sha256='506f731b3886def158c15fd8b74fa98390f304a507d2040972e6b09ddefac8f0') - version('0.5.3', sha256='d45b569fe3aa5934883bc7216c243d53168351c23e020d96a46fa77a1563b65e') + version("0.5.4", sha256="506f731b3886def158c15fd8b74fa98390f304a507d2040972e6b09ddefac8f0") + version("0.5.3", sha256="d45b569fe3aa5934883bc7216c243d53168351c23e020d96a46fa77a1563b65e") - depends_on('perl@5.10.0:') + depends_on("perl@5.10.0:") # bamtools needs to build before the others. parallel = False - @run_before('install') + @run_before("install") def filter_sbang(self): """Run before install so that the standard Spack sbang install hook can fix up the path to the perl|python binary. """ with working_dir(self.stage.source_path): - kwargs = {'ignore_absent': True, 'backup': False, 'string': False} + kwargs = {"ignore_absent": True, "backup": False, "string": False} - match = '^#!/usr/bin/env perl' - perl = self.spec['perl'].command + match = "^#!/usr/bin/env perl" + perl = self.spec["perl"].command substitute = "#!{perl}".format(perl=perl) - files = ['FindDenovos.pl', 'scalpel-export', - 'scalpel-discovery', 'FindVariants.pl', - 'FindSomatic.pl'] + files = [ + "FindDenovos.pl", + "scalpel-export", + "scalpel-discovery", + "FindVariants.pl", + "FindSomatic.pl", + ] filter_file(match, substitute, *files, **kwargs) # Scalpel doesn't actually *have* an install step. The authors @@ -51,32 +55,41 @@ class Scalpel(MakefilePackage, SourceforgePackage): # bits into prefix.bin. It's not normal, but.... # def install(self, spec, prefix): - destdir = prefix.bin # see the note above.... + destdir = prefix.bin # see the note above.... mkdirp(destdir) - files = ['FindSomatic.pl', 'HashesIO.pm', 'MLDBM.pm', - 'scalpel-export', 'Utils.pm', 'FindDenovos.pl', - 'FindVariants.pl', 'scalpel-discovery', - 'SequenceIO.pm', 'Usage.pm'] + files = [ + "FindSomatic.pl", + "HashesIO.pm", + "MLDBM.pm", + "scalpel-export", + "Utils.pm", + "FindDenovos.pl", + "FindVariants.pl", + "scalpel-discovery", + "SequenceIO.pm", + "Usage.pm", + ] for f in files: install(f, destdir) - dirs = ['Text', 'MLDBM', 'Parallel', ] + dirs = [ + "Text", + "MLDBM", + "Parallel", + ] for d in dirs: install_tree(d, join_path(destdir, d)) - install_tree('bamtools-2.3.0/bin', - join_path(destdir, 'bamtools-2.3.0', 'bin')) - install_tree('bamtools-2.3.0/lib', - join_path(destdir, 'bamtools-2.3.0', 'lib')) + install_tree("bamtools-2.3.0/bin", join_path(destdir, "bamtools-2.3.0", "bin")) + install_tree("bamtools-2.3.0/lib", join_path(destdir, "bamtools-2.3.0", "lib")) - mkdirp(join_path(destdir, 'bcftools-1.1')) - install('bcftools-1.1/bcftools', join_path(destdir, 'bcftools-1.1')) + mkdirp(join_path(destdir, "bcftools-1.1")) + install("bcftools-1.1/bcftools", join_path(destdir, "bcftools-1.1")) - mkdirp(join_path(destdir, 'Microassembler')) - install('Microassembler/Microassembler', - join_path(destdir, 'Microassembler')) + mkdirp(join_path(destdir, "Microassembler")) + install("Microassembler/Microassembler", join_path(destdir, "Microassembler")) - mkdirp(join_path(destdir, 'samtools-1.1')) - install('samtools-1.1/samtools', join_path(destdir, 'samtools-1.1')) + mkdirp(join_path(destdir, "samtools-1.1")) + install("samtools-1.1/samtools", join_path(destdir, "samtools-1.1")) |