def generate_activate_file(print_env,
deploy_dir,
append_to_bashrc=False,
append_to_bashprofile=False):
log.info('Generating activate.sh file')
lines = []
for env_name in print_env:
old_var = print_env[env_name]
if (env_name.upper() == 'PATH') or \
(env_name.upper() == 'PYTHONPATH'):
new_var = old_var + ':$%s' % env_name.upper()
else:
new_var = old_var
var_string = 'export %s=%s' % (env_name, new_var)
var_string += '\n'
lines.append(var_string)
output_file = os.path.join(deploy_dir, 'activate.sh')
old_contents = []
if os.path.exists(output_file):
oldFile = open(output_file, 'r')
old_contents = oldFile.readlines()
oldFile.close()
if lines != old_contents:
util.backup_file(output_file)
if os.path.exists(output_file):
os.remove(output_file)
util.write_new_file(output_file, lines)
appendStr = 'echo "source %s" >> ~/.bashrc' % output_file
appendFile = '~/.bashrc'
compStr = 'source %s\n' % output_file
if (append_to_bashrc) and (not util.line_in_file(compStr, appendFile)):
log.debug('Appending environment settings to ~/.bashrc')
(appendStatus, appendOut) = commands.getstatusoutput(appendStr)
if appendStatus != 0:
log.error('Error appending to ~/.bashrc')
log.error('Output:')
log.error(appendOut)
else:
log.info('Successfully appended to ~/.bashrc')
appendStr = 'echo "source %s" >> ~/.bash_profile' % output_file
appendFile = '~/.bash_profile'
compStr = 'source %s\n' % output_file
if (append_to_bashprofile) and (not util.line_in_file(compStr,
appendFile)):
log.debug('Appending environment settings to ~/.bash_profile')
(appendStatus, appendOut) = commands.getstatusoutput(appendStr)
if appendStatus != 0:
log.error('Error appending to ~/.bash_profile')
log.error('Output:')
log.error(appendOut)
else:
log.info('Successfully appended to ~/.bash_profile')
def generate_activate_file(print_env,
deploy_dir,
append_to_bashrc=False,
append_to_bashprofile=False):
log.info('Generating activate.sh file')
lines = []
for env_name in print_env:
old_var = print_env[env_name]
if (env_name.upper() == 'PATH') or \
(env_name.upper() == 'PYTHONPATH'):
new_var = old_var + ':$%s' % env_name.upper()
else:
new_var = old_var
var_string = 'export %s=%s' % (env_name, new_var)
var_string += '\n'
lines.append(var_string)
output_file = os.path.join(deploy_dir, 'activate.sh')
old_contents = []
if os.path.exists(output_file):
oldFile = open(output_file, 'r')
old_contents = oldFile.readlines()
oldFile.close()
if lines != old_contents:
util.backup_file(output_file)
if os.path.exists(output_file):
os.remove(output_file)
util.write_new_file(output_file, lines)
appendStr = 'echo "source %s" >> ~/.bashrc' % output_file
appendFile = '~/.bashrc'
compStr = 'source %s\n' % output_file
if (append_to_bashrc) and (not util.line_in_file(compStr, appendFile)):
log.debug('Appending environment settings to ~/.bashrc')
(appendStatus, appendOut) = commands.getstatusoutput(appendStr)
if appendStatus != 0:
log.error('Error appending to ~/.bashrc')
log.error('Output:')
log.error(appendOut)
else:
log.info('Successfully appended to ~/.bashrc')
appendStr = 'echo "source %s" >> ~/.bash_profile' % output_file
appendFile = '~/.bash_profile'
compStr = 'source %s\n' % output_file
if (append_to_bashprofile) and (not util.line_in_file(compStr, appendFile)):
log.debug('Appending environment settings to ~/.bash_profile')
(appendStatus, appendOut) = commands.getstatusoutput(appendStr)
if appendStatus != 0:
log.error('Error appending to ~/.bash_profile')
log.error('Output:')
log.error(appendOut)
else:
log.info('Successfully appended to ~/.bash_profile')
def _generate_qiime_config(python_path, deploy_dir, all_apps_to_deploy, log,
qiime_config_path):
qiime_path = None
blast_path = None
blast_data_path = None
deploy_dir_contents = os.listdir(deploy_dir)
for app in all_apps_to_deploy:
if app.name == 'qiime':
qiime_path = os.path.join(app.deploy_dir, 'bin')
if app.name == 'blast':
blast_path = os.path.join(app.deploy_dir, 'bin/blastall')
blast_data_path = os.path.join(app.deploy_dir, 'data')
log.info('Generating new %s file' % qiime_config_path)
lines = []
lines.append('# autogenerated by qiime-deploy\n')
if qiime_path:
# If we have a [qiime] target, write out additional QIIME config lines
# for qiime_scripts_dir, etc.. These values have since been removed (or
# replaced by defaults) in QIIME, but we'll continue to write them here
# to maintain backwards compatibility with older qiime-deploy conf
# files that still deploy QIIME instead of assuming that QIIME's python
# code is already installed (e.g., via pip).
line = 'qiime_scripts_dir\t%s\n' % qiime_path
lines.append(line)
line = 'python_exe_fp\t%s\n' % python_path
lines.append(line)
lines.append('working_dir\t/tmp/\n')
lines.append('temp_dir\t/tmp/\n')
# for n3phele
lines.append('cloud_environment\tFalse\n')
path = deploy_dir + '/lanemask_in_1s_and_0s'
line = 'template_alignment_lanemask_fp\t%s\n' % path
lines.append(line)
path = deploy_dir + '/core_set_aligned.fasta.imputed'
line = 'pynast_template_alignment_fp\t%s\n' % path
lines.append(line)
# lines for Greengenes files
path = deploy_dir + '/gg_otus-13_8-release/rep_set/97_otus.fasta'
line = 'assign_taxonomy_reference_seqs_fp\t%s\n' % path
lines.append(line)
path = deploy_dir + '/gg_otus-13_8-release/taxonomy/97_otu_taxonomy.txt'
line = 'assign_taxonomy_id_to_taxonomy_fp\t%s\n' % path
lines.append(line)
parallel_jobs_path = os.path.join(qiime_path, 'start_parallel_jobs.py')
lines.append('cluster_jobs_fp\t%s\n' % parallel_jobs_path)
# The following QIIME config values are set regardless of whether we're
# deploying the latest QIIME or previous versions.
if blast_path:
line = 'blastall_fp\t%s\n' % blast_path
lines.append(line)
if blast_data_path:
line = 'blastmat_dir\t%s\n' % blast_data_path
lines.append(line)
lines.append('')
lines.append('')
old_contents = []
if os.path.exists(qiime_config_path):
oldFile = open(qiime_config_path, 'r')
old_contents = oldFile.readlines()
oldFile.close()
if lines != old_contents:
util.backup_file(qiime_config_path)
if os.path.exists(qiime_config_path):
os.remove(qiime_config_path)
util.write_new_file(qiime_config_path, lines)
log.info('Generated new %s file' % qiime_config_path)
return 0
def _generate_qiime_config(python_path, deploy_dir, all_apps_to_deploy, log):
qiime_path = None
blast_path = None
blast_data_path = None
deploy_dir_contents = os.listdir(deploy_dir)
for app in all_apps_to_deploy:
if app.name == 'qiime':
qiime_path = os.path.join(app.deploy_dir, 'bin')
if app.name == 'blast':
blast_path = os.path.join(app.deploy_dir, 'bin/blastall')
blast_data_path = os.path.join(app.deploy_dir, 'data')
if not qiime_path:
# No qiime target so skip.
return 0
qiime_config_path = os.path.join(deploy_dir, 'qiime_config')
log.info('Generating new %s file' % qiime_config_path)
if not (blast_path and blast_data_path):
log.error('Missing necessary paths for %s file.' % qiime_config_path)
log.error('Skipping generation of %s' % qiime_config_path)
return 1
lines = []
lines.append('# autogenerated by qiime-deploy\n')
parallel_jobs_path = os.path.join(qiime_path, 'start_parallel_jobs.py')
lines.append('cluster_jobs_fp\t%s\n' % parallel_jobs_path)
line = 'python_exe_fp\t%s\n' % python_path
lines.append(line)
line = 'qiime_scripts_dir\t%s\n' % qiime_path
lines.append(line)
line = 'blastmat_dir\t%s\n' % blast_data_path
lines.append(line)
line = 'blastall_fp\t%s\n' % blast_path
lines.append(line)
path = deploy_dir + '/lanemask_in_1s_and_0s'
line = 'template_alignment_lanemask_fp\t%s\n' % path
lines.append(line)
path = deploy_dir + '/core_set_aligned.fasta.imputed'
line = 'pynast_template_alignment_fp\t%s\n' % path
lines.append(line)
#line = 'pyronoise_data_fp\t%s' % denoiser_path
#lines.append(line)
lines.append('pynast_template_alignment_blastdb\t\n')
lines.append('working_dir\t/tmp/\n')
lines.append('jobs_to_start\t1\n')
lines.append('seconds_to_sleep\t60\n')
lines.append('temp_dir\t/tmp/\n')
# lines for n3phele
lines.append('cloud_environment\tFalse\n')
#lines for Greengenes files
path = deploy_dir + '/gg_otus-12_10-release/rep_set/97_otus.fasta'
line = 'assign_taxonomy_reference_seqs_fp\t%s\n' % path
lines.append(line)
path = deploy_dir + '/gg_otus-12_10-release/taxonomy/97_otu_taxonomy.txt'
line = 'assign_taxonomy_id_to_taxonomy_fp\t%s\n' % path
lines.append(line)
lines.append('')
lines.append('')
old_contents = []
if os.path.exists(qiime_config_path):
oldFile = open(qiime_config_path, 'r')
old_contents = oldFile.readlines()
oldFile.close()
if lines != old_contents:
util.backup_file(qiime_config_path)
if os.path.exists(qiime_config_path):
os.remove(qiime_config_path)
util.write_new_file(qiime_config_path, lines)
log.info('Generated new %s file' % qiime_config_path)
return 0