+++ /dev/null
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
-import arvados
-import re
-import os
-import sys
-import fcntl
-import subprocess
-
-bwa_install_path = None
-
-def install_path():
- """
- Extract the bwa source tree, build the bwa binary, and return the
- path to the source tree.
- """
- global bwa_install_path
- if bwa_install_path:
- return bwa_install_path
-
- bwa_install_path = arvados.util.tarball_extract(
- tarball = arvados.current_job()['script_parameters']['bwa_tbz'],
- path = 'bwa')
-
- # build "bwa" binary
- lockfile = open(os.path.split(bwa_install_path)[0] + '.bwa-make.lock',
- 'w')
- fcntl.flock(lockfile, fcntl.LOCK_EX)
- arvados.util.run_command(['make', '-j16'], cwd=bwa_install_path)
- lockfile.close()
-
- return bwa_install_path
-
-def bwa_binary():
- """
- Return the path to the bwa executable.
- """
- return os.path.join(install_path(), 'bwa')
-
-def run(command, command_args, **kwargs):
- """
- Build and run the bwa binary.
-
- command is the bwa module, e.g., "index" or "aln".
-
- command_args is a list of additional command line arguments, e.g.,
- ['-a', 'bwtsw', 'ref.fasta']
-
- It is assumed that we are running in a Crunch job environment, and
- the job's "bwa_tbz" parameter is a collection containing the bwa
- source tree in a .tbz file.
- """
- execargs = [bwa_binary(),
- command]
- execargs += command_args
- sys.stderr.write("%s.run: exec %s\n" % (__name__, str(execargs)))
- arvados.util.run_command(
- execargs,
- cwd=arvados.current_task().tmpdir,
- stderr=sys.stderr,
- stdin=kwargs.get('stdin', subprocess.PIPE),
- stdout=kwargs.get('stdout', sys.stderr))
-
-def one_task_per_pair_input_file(if_sequence=0, and_end_task=True):
- """
- Queue one task for each pair of fastq files in this job's input
- collection.
-
- Each new task will have two parameters, named "input_1" and
- "input_2", each being a manifest containing a single fastq file.
-
- A matching pair of files in the input collection is assumed to
- have names "x_1.y" and "x_2.y".
-
- Files in the input collection that are not part of a matched pair
- are silently ignored.
-
- if_sequence and and_end_task arguments have the same significance
- as in arvados.job_setup.one_task_per_input_file().
- """
- if if_sequence != arvados.current_task()['sequence']:
- return
- job_input = arvados.current_job()['script_parameters']['input']
- cr = arvados.CollectionReader(job_input)
- all_files = []
- for s in cr.all_streams():
- all_files += list(s.all_files())
- for s in cr.all_streams():
- for left_file in s.all_files():
- left_name = left_file.name()
- right_file = None
- right_name = re.sub(r'(.*_)1\.', '\g<1>2.', left_name)
- if right_name == left_name:
- continue
- for f2 in s.all_files():
- if right_name == f2.name():
- right_file = f2
- if right_file != None:
- new_task_attrs = {
- 'job_uuid': arvados.current_job()['uuid'],
- 'created_by_job_task_uuid': arvados.current_task()['uuid'],
- 'sequence': if_sequence + 1,
- 'parameters': {
- 'input_1':left_file.as_manifest(),
- 'input_2':right_file.as_manifest()
- }
- }
- arvados.api().job_tasks().create(body=new_task_attrs).execute()
- if and_end_task:
- arvados.api().job_tasks().update(uuid=arvados.current_task()['uuid'],
- body={'success':True}
- ).execute()
- exit(0)
projects / arvados.git / blobdiff