/usr/bin/bowtie2-build is in bowtie2 2.3.4.1-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 | #!/usr/bin/env python
"""
Copyright 2014, Ben Langmead <langmea@cs.jhu.edu>
This file is part of Bowtie 2.
Bowtie 2 is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Bowtie 2 is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
"""
import os
import sys
import inspect
import logging
import argparse
import subprocess
from collections import deque
def main():
parser = argparse.ArgumentParser()
group = parser.add_mutually_exclusive_group()
group.add_argument('--debug', action='store_true')
group.add_argument('--sanitized', action='store_true')
parser.add_argument('--verbose', action='store_true')
parser.add_argument('--large-index', action='store_true')
logging.basicConfig(level=logging.ERROR,
format='%(levelname)s: %(message)s'
)
delta = 200
small_index_max_size= 4 * 1024**3 - delta
build_bin_name = 'bowtie2-build'
build_bin_s = 'bowtie2-build-s'
build_bin_l = 'bowtie2-build-l'
curr_script = os.path.realpath(inspect.getsourcefile(main))
ex_path = os.path.dirname(curr_script)
build_bin_spec = os.path.join(ex_path,build_bin_s)
script_options, argv = parser.parse_known_args()
argv = deque(argv)
if script_options.verbose:
logging.getLogger().setLevel(logging.INFO)
if script_options.debug:
build_bin_spec += '-debug'
build_bin_l += '-debug'
if script_options.sanitized:
build_bin_spec += '-sanitized'
build_bin_l += '-sanitized'
if script_options.large_index:
build_bin_spec = os.path.join(ex_path,build_bin_l)
elif len(argv) >= 2:
ref_fnames = argv[-2]
tot_size = 0
for fn in ref_fnames.split(','):
if os.path.exists(fn):
statinfo = os.stat(fn)
tot_size += statinfo.st_size
if tot_size > small_index_max_size:
build_bin_spec = os.path.join(ex_path,build_bin_l)
argv.appendleft('basic-0')
argv.appendleft('--wrapper')
argv.appendleft(build_bin_spec)
logging.info('Command: %s' % ' '.join(argv))
subprocess.call(argv)
if __name__ == '__main__':
main()
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