# Submit the Beta Diversity jobs
try:
# Attempt the submission
submitQiimeJob(meta_id, user_id, job_type, job_input, data_access)
except Exception, e:
raise ValueError,e
# Generate and Submit Heatmap Job
if 'heatmap' in analyses_to_start:
job_type='makeOTUHeatmap'
# Submit the Beta Diversity jobs
try:
# Attempt the submission
submitQiimeJob(meta_id, user_id, job_type, job_input, data_access)
except Exception, e:
raise ValueError,e
# Generate and Submit Alpha-Diversity Job
if 'arare' in analyses_to_start:
job_type='alphaRarefaction'
# Submit the Alpha Diversity jobs
try:
# Attempt the submission
submitQiimeJob(meta_id, user_id, job_type, job_input, data_access)
except Exception, e:
raise ValueError,e
def run_other_qiime_analysis(data_access, fs_fp, web_fp, otu_table_filepath,
map_filepath, file_name_prefix, user_id, meta_id,
params_path, rarefied_at, jobs_to_start, tree_fp,
zip_fpath, zip_fpath_db):
# get the date to put in the db
run_date=datetime.now().strftime("%d/%m/%Y/%H/%M/%S")
# Prepare the params for submitting new jobs to the torque-poller
params=[]
params.append('fs_fp=%s' % fs_fp)
params.append('web_fp=%s' % web_fp)
params.append('otu_table_fp=%s' % otu_table_filepath)
params.append('mapping_file_fp=%s' % map_filepath)
params.append('fname_prefix=%s' % file_name_prefix)
params.append('user_id=%s' % user_id)
params.append('meta_id=%s' % meta_id)
params.append('params_path=%s' % params_path)
params.append('bdiv_rarefied_at=%s' % rarefied_at)
params.append('jobs_to_start=%s' % jobs_to_start)
params.append('tree_fp=%s' % tree_fp)
params.append('run_date=%s' % run_date)
params.append('zip_fpath=%s' % zip_fpath)
params.append('zip_fpath_db=%s' % zip_fpath_db)
job_input='!!'.join(params)
# Determine which meta-analyses the user selected
analyses_to_start=jobs_to_start.split(',')
# Prepare TopiaryExplorer job
if 'showTE' in analyses_to_start:
tree_fpath=path.abspath('%s/software/gg_otus_4feb2011/trees/gg_97_otus_4feb2011.tre' % (os.environ['HOME']))
python_exe_fp = qiime_config['python_exe_fp']
commands=[]
command_handler=call_commands_serially
status_update_callback=no_status_updates
logger = WorkflowLogger(generate_log_fp('/tmp/'),
params=dict(''),
qiime_config=qiime_config)
#define topiary explorer fpaths
jnlp_fname=path.splitext(path.split(otu_table_filepath)[-1])[0]+'.jnlp'
tep_fname=path.splitext(path.split(otu_table_filepath)[-1])[0] + '.tep'
jnlp_filepath_web=path.join(web_fp, 'topiaryexplorer_files', jnlp_fname)
jnlp_filepath_web_tep=path.join(web_fp,'topiaryexplorer_files',
tep_fname)
# define the hard-link for the JNLP
if ServerConfig.home=='/home/wwwdevuser/':
host_name='http://webdev.microbio.me/qiime'
else:
host_name='http://www.microbio.me/qiime'
jnlp_filepath_web_tep_url=path.join(host_name, jnlp_filepath_web_tep)
output_dir=os.path.join(fs_fp, 'topiaryexplorer_files')
#build command
make_tep_cmd='%s %s/make_tep.py -i %s -m %s -t %s -o %s -u %s -w' %\
(python_exe_fp, script_dir, otu_table_filepath, map_filepath,
tree_fpath, output_dir, jnlp_filepath_web_tep_url)
commands.append([('Make TopiaryExplorer jnlp', make_tep_cmd)])
# Call the command handler on the list of commands
command_handler(commands, status_update_callback, logger)
#zip Topiary Explorer jnlp file
cmd_call='cd %s; zip %s %s' % (output_dir,zip_fpath,jnlp_fname)
system(cmd_call)
#zip Topiary Explorer project file
cmd_call='cd %s; zip %s %s' % (output_dir,zip_fpath,tep_fname)
system(cmd_call)
valid=data_access.addMetaAnalysisFiles(True, int(meta_id),
jnlp_filepath_web, 'OTUTABLE',
run_date, 'TOPIARYEXPLORER')
if not valid:
raise ValueError, 'There was an issue uploading the filepaths to the DB!'
# Generate and Submit Beta-Diversity Job
if 'bdiv' in analyses_to_start:
job_type='betaDiversityThroughPlots'
# Submit the Beta Diversity jobs
try:
# Attempt the submission
submitQiimeJob(meta_id, user_id, job_type, job_input, data_access)
except Exception, e:
raise ValueError,e
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
submit_to_test_db=opts.submit_to_test_db
fasta_file_paths=opts.fasta_file_paths
study_id=opts.study_id
output_dir=opts.output_dir
platform=opts.platform
user_id=opts.user_id
if submit_to_test_db == 'False':
# Load the data into the database
data_access = data_access_factory(ServerConfig.data_access_type)
else:
# Load the data into the database
data_access = data_access_factory(DataAccessType.qiime_test)
# Get all of the fasta files
if (platform=='FLX' or platform=='TITANIUM'):
print 'Submitting SFF data to database...'
analysis_id, input_dir, seq_run_id, split_lib_input_md5sum = \
submit_sff_and_split_lib(data_access, fasta_file_paths, study_id)
elif platform=='ILLUMINA':
print 'Submitting Illumina data to database...'
analysis_id, input_dir, seq_run_id, split_lib_input_md5sum = \
submit_illumina_and_split_lib(data_access, fasta_file_paths,
study_id,output_dir)
elif platform=='FASTA':
print 'Submitting FASTA data to database...'
analysis_id, input_dir, seq_run_id, split_lib_input_md5sum = \
submit_fasta_and_split_lib(data_access, fasta_file_paths,
study_id, output_dir)
'''
# Submit Split-library loading job
split_library_id=load_split_lib_sequences(data_access,input_dir,
analysis_id, seq_run_id,
split_lib_input_md5sum)
'''
# verify that these are not metagenomic sequences
# otherwise load the OTU table
study_info=data_access.getStudyInfo(study_id,user_id)
if study_info['investigation_type'].lower() == 'metagenome':
# skip OTU loading
pass
else:
print 'Submitting OTU data to database...'
load_otu_mapping(data_access, output_dir, analysis_id)
params=[]
params.append('OutputDir=%s' % output_dir)
params.append('UserId=%s' % user_id)
params.append('StudyId=%s' % study_id)
params.append('TestDB=%s' % submit_to_test_db)
params.append('ProcessedFastaFilepath=%s' % (fasta_file_paths))
params.append('AnalysisId=%s' % analysis_id)
params.append('SeqRunId=%s' % seq_run_id)
params.append('MDchecksum=%s' % split_lib_input_md5sum)
job_input='!!'.join(params)
job_type='LoadSplitLibSeqsHandler'
submitQiimeJob(study_id, user_id, job_type, job_input, data_access)
print 'Completed database loading.'