<commit_before># Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack import *


class Scalpel(MakefilePackage):
    """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.
    """

    homepage = "http://scalpel.sourceforge.net/index.html"
    url      = "https://downloads.sourceforge.net/project/scalpel/scalpel-0.5.3.tar.gz"

    version('0.5.3', '682c9f1cd6ab2cb11c6866f303c673f0')

    depends_on('cmake')
    depends_on('perl@5.10.0:')

    # bamtools needs to build before the others.
    parallel = False

    @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}

            match = '^#!/usr/bin/env perl'
            perl = self.spec['perl'].command
            substitute = "#!{perl}".format(perl=perl)
            files = ['FindDenovos.pl', 'scalpel-export',
                     'scalpel-discovery', 'FindVariants.pl',<commit_msg>Scalpel package: remove CMake dependency (#12631)<commit_after># Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack import *


class Scalpel(MakefilePackage):
    """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.
    """

    homepage = "http://scalpel.sourceforge.net/index.html"
    url      = "https://downloads.sourceforge.net/project/scalpel/scalpel-0.5.3.tar.gz"

    version('0.5.3', '682c9f1cd6ab2cb11c6866f303c673f0')

    depends_on('perl@5.10.0:')

    # bamtools needs to build before the others.
    parallel = False

    @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}

            match = '^#!/usr/bin/env perl'
            perl = self.spec['perl'].command
            substitute = "#!{perl}".format(perl=perl)
            files = ['FindDenovos.pl', 'scalpel-export',
                     'scalpel-discovery', 'FindVariants.pl',
{'fraction_non_alphanumeric': 0.11519434628975266, 'fraction_numerical': 0.030035335689045935, 'mean_word_length': 2.926490984743412, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4258785', 'n_tokens_mistral': 931, 'n_tokens_neox': 844, 'n_words': 231}