/usr/bin/bowtie-build is in bowtie 1.1.2-3.
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 87 88 89 90 91 92 93 94 95 | #!/usr/bin/env python
"""
Copyright 2014, Ben Langmead <langmea@cs.jhu.edu>
This file is part of Bowtie.
Bowtie 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 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. If not, see <http://www.gnu.org/licenses/>.
"""
import os
import sys
import inspect
import logging
def build_args():
"""
Parse the wrapper arguments. Returns the options,<programm arguments> tuple.
"""
parsed_args = {}
to_remove = []
argv = sys.argv[:]
for i, arg in enumerate(argv):
if arg == '--large-index':
parsed_args[arg] = ""
to_remove.append(i)
elif arg == '--debug':
parsed_args[arg] = ""
to_remove.append(i)
elif arg == '--verbose':
parsed_args[arg] = ""
to_remove.append(i)
for i in reversed(to_remove):
del argv[i]
return parsed_args, argv
def main():
logging.basicConfig(level=logging.ERROR,
format='%(levelname)s: %(message)s'
)
delta = 200
small_index_max_size= 4 * 1024**3 - delta
build_bin_name = "bowtie-build"
build_bin_s = "bowtie-build-s"
build_bin_l = "bowtie-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)
options, argv = build_args()
if '--verbose' in options:
logging.getLogger().setLevel(logging.INFO)
if '--debug' in options:
build_bin_spec += '-debug'
build_bin_l += '-debug'
if '--large-index' in options:
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[0] = build_bin_name
argv.insert(1, 'basic-0')
argv.insert(1, '--wrapper')
logging.info('Command: %s %s' % (build_bin_spec, ' '.join(argv[1:])))
os.execv(build_bin_spec, argv)
if __name__ == "__main__":
main()
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