def __init__(self, main, app):
'''
Execute actions correspending to the creation of a "FormInstallBioinfoApp" instance.
'''
# save initial parameters in instance variables
self.main = main
self.root = main.root
self.container = main.container
self.app_code = app
# call the init method of the parent class
tkinter.Frame.__init__(self, self.container)
# set cursor to show busy status
self.root.config(cursor='watch')
self.root.update()
# set the software name
if self.app_code == xlib.get_blastplus_code():
self.app_name = xlib.get_blastplus_name()
elif self.app_code == xlib.get_diamond_code():
self.app_name = xlib.get_diamond_name()
elif self.app_code == xlib.get_entrez_direct_code():
self.app_name = xlib.get_entrez_direct_name()
elif self.app_code == xlib.get_miniconda3_code():
self.app_name = xlib.get_miniconda3_name()
elif self.app_code == xlib.get_r_code():
self.app_name = xlib.get_r_name()
elif self.app_code == xlib.get_transdecoder_code():
self.app_name = xlib.get_transdecoder_name()
# assign the text of the "head"
self.head = f'{self.app_name} - Install software'
# create the wrappers to track changes in the inputs
pass
# build the graphical user interface
self.build_gui()
# load initial data in inputs
self.initialize_inputs()
# set cursor to show normal status
self.root.config(cursor='')
self.root.update()
def build_menu_bioinfo_software_installation():
'''
Build the menu Bioinfo software installation.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment('Bioinfo software installation')
# print the menu options
print( 'Options:')
print()
print(f' 1. {xlib.get_miniconda3_name()} (Conda infrastructure)')
print()
print(f' 2. {xlib.get_blastplus_name()}'.format())
print(f' 3. {xlib.get_diamond_name()}')
print(f' 4. {xlib.get_entrez_direct_name()}')
print(f' 5. {xlib.get_transdecoder_name()}')
# -- print()
# -- print(f' X. {xlib.get_r_name()} & analysis packages')
print()
print( ' X. Return to menu Main')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
cbioinfoapp.form_install_bioinfo_app(xlib.get_miniconda3_code())
elif option == '2':
cbioinfoapp.form_install_bioinfo_app(xlib.get_blastplus_code())
elif option == '3':
cbioinfoapp.form_install_bioinfo_app(xlib.get_diamond_code())
elif option == '4':
cbioinfoapp.form_install_bioinfo_app(xlib.get_entrez_direct_code())
elif option == '5':
cbioinfoapp.form_install_bioinfo_app(xlib.get_transdecoder_code())
# -- elif option == 'X':
# -- cbioinfoapp.form_install_bioinfo_app(xlib.get_r_code())
elif option == 'X':
break
def execute(self, event=None):
'''
Execute the list the result logs in the cluster.
'''
# if "button_execute" is disabled, exit function
if str(self.button_execute['state']) == 'disabled':
return
# check inputs
OK = self.check_inputs()
if not OK:
message = 'Some input values are not OK.'
tkinter.messagebox.showerror(
f'{xlib.get_short_project_name()} - {self.head}', message)
# get the dictionary of TOA configuration.
if OK:
toa_config_dict = xtoa.get_toa_config_dict()
# get the run dictionary
if OK:
process_type_dir = f'{toa_config_dict["RESULT_DIR"]}/{self.wrapper_process_type.get()}'
subdir_list = [
subdir for subdir in os.listdir(process_type_dir)
if os.path.isdir(os.path.join(process_type_dir, subdir))
]
result_dataset_dict = {}
for subdir in subdir_list:
result_dataset_id = subdir
try:
pattern = r'^(.+)\-(.+)\-(.+)$'
mo = re.search(pattern, result_dataset_id)
bioinfo_app_code = mo.group(1).strip()
yymmdd = mo.group(2)
hhmmss = mo.group(3)
date = f'20{yymmdd[:2]}-{yymmdd[2:4]}-{yymmdd[4:]}'
time = f'{hhmmss[:2]}:{hhmmss[2:4]}:{hhmmss[4:]}'
except:
bioinfo_app_code = 'xxx'
date = '0000-00-00'
time = '00:00:00'
if result_dataset_id.startswith(xlib.get_blastplus_code() +
'-'):
bioinfo_app_name = xlib.get_blastplus_name()
elif result_dataset_id.startswith(xlib.get_diamond_code() +
'-'):
bioinfo_app_name = xlib.get_diamond_name()
elif result_dataset_id.startswith(
xlib.get_entrez_direct_code() + '-'):
bioinfo_app_name = xlib.get_entrez_direct_name()
elif result_dataset_id.startswith(xlib.get_miniconda3_code() +
'-'):
bioinfo_app_name = xlib.get_miniconda3_name()
elif result_dataset_id.startswith(xlib.get_r_code() + '-'):
bioinfo_app_name = xlib.get_r_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_download_basic_data_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_basic_data_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_dicots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_dicots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_gene_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_gene_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_go_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_go_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_download_gymno_01_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_gymno_01_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_interpro_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_interpro_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_monocots_04_code() +
'-'):
bioinfo_app_name = xlib.get_toa_process_download_monocots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_taxonomy_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_taxonomy_name(
)
elif result_dataset_id.startswith(
xlib.
get_toa_process_gilist_viridiplantae_nucleotide_gi_code(
) + '-'):
bioinfo_app_name = xlib.get_toa_process_gilist_viridiplantae_nucleotide_gi_name(
)
elif result_dataset_id.startswith(
xlib.
get_toa_process_gilist_viridiplantae_protein_gi_code()
+ '-'):
bioinfo_app_name = xlib.get_toa_process_gilist_viridiplantae_protein_gi_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_basic_data_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_basic_data_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_dicots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_dicots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_gene_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_gene_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_load_go_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_go_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_load_gymno_01_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_gymno_01_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_interpro_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_interpro_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_monocots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_monocots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_merge_annotations_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_merge_annotations_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_nr_blastplus_db_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_nr_blastplus_db_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_nr_diamond_db_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_nr_diamond_db_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_nt_blastplus_db_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_nt_blastplus_db_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_pipeline_aminoacid_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_pipeline_aminoacid_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_pipeline_nucleotide_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_pipeline_nucleotide_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_dicots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_proteome_dicots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_gymno_01_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_proteome_gymno_01_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_monocots_04_code() +
'-'):
bioinfo_app_name = xlib.get_toa_process_proteome_monocots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_refseq_plant_code() +
'-'):
bioinfo_app_name = xlib.get_toa_process_proteome_refseq_plant_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_rebuild_toa_database_code() +
'-'):
bioinfo_app_name = xlib.get_get_toa_process_rebuild_toa_database_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_recreate_toa_database_code() +
'-'):
bioinfo_app_name = xlib.get_get_toa_process_recreate_toa_database_name(
)
elif result_dataset_id.startswith(
xlib.get_transdecoder_code() + '-'):
bioinfo_app_name = xlib.get_transdecoder_name()
else:
bioinfo_app_name = 'xxx'
status_ok = os.path.isfile(
xlib.get_status_ok(os.path.join(process_type_dir, subdir)))
status_wrong = os.path.isfile(
xlib.get_status_wrong(
os.path.join(process_type_dir, subdir)))
if status_ok and not status_wrong:
status = 'OK'
elif not status_ok and status_wrong:
status = 'wrong'
elif not status_ok and not status_wrong:
status = 'not finished'
elif status_ok and status_wrong:
status = 'undetermined'
key = f'{bioinfo_app_name}-{result_dataset_id}'
result_dataset_dict[key] = {
'process_type': self.wrapper_process_type.get(),
'bioinfo_app': bioinfo_app_name,
'result_dataset_id': result_dataset_id,
'date': date,
'time': time,
'status': status
}
# check if there are any nodes running
if OK:
if result_dataset_dict == {}:
message = 'There is not any run.'
tkinter.messagebox.showwarning(
f'{xlib.get_short_project_name()} - {self.head}', message)
# build the data list
if OK:
data_list = [
'process_type', 'bioinfo_app', 'result_dataset_id', 'date',
'time', 'status'
]
# build the data dictionary
if OK:
data_dict = {}
data_dict['process_type'] = {
'text': 'Process type',
'width': 180,
'alignment': 'left'
}
data_dict['bioinfo_app'] = {
'text': 'Bioinfo app / Utility',
'width': 340,
'alignment': 'left'
}
data_dict['result_dataset_id'] = {
'text': 'Result dataset',
'width': 225,
'alignment': 'left'
}
data_dict['date'] = {
'text': 'Date',
'width': 95,
'alignment': 'right'
}
data_dict['time'] = {
'text': 'Time',
'width': 75,
'alignment': 'right'
}
data_dict['status'] = {
'text': 'Status',
'width': 90,
'alignment': 'left'
}
# create the dialog Table to show the nodes running
if OK:
dialog_table = gdialogs.DialogTable(
self,
f'Runs in {xlib.get_result_dir()}/{self.wrapper_process_type.get()}',
400, 1030, data_list, data_dict, result_dataset_dict,
sorted(result_dataset_dict.keys()), 'view_result_logs',
['revisar'])
self.wait_window(dialog_table)
# close the form
if OK:
self.close()
def execute(self, event=None):
'''
Execute the app installation process.
'''
# if "button_execute" is disabled, exit function
if str(self.button_execute['state']) == 'disabled':
return
# check inputs
OK = self.check_inputs()
if not OK:
message = 'Some input values are not OK.'
tkinter.messagebox.showerror(
f'{xlib.get_short_project_name()} - {self.head}', message)
# confirm the software installation
if OK:
if self.app_code == xlib.get_miniconda3_code():
message = f'{self.app_name} (Conda infrastructure) is going to be installed. All Conda packages previously installed will be lost and they have to be reinstalled.\n\nAre you sure to continue?'
elif self.app_code == xlib.get_r_code():
message = f'{self.app_name} and analysis packages are going to be installed. The previous version will be lost, if it exists.\n\nAre you sure to continue?'
else:
message = f'The {self.app_name} Conda package is going to be installed. The previous version will be lost, if it exists.\n\nAre you sure to continue?'
OK = tkinter.messagebox.askyesno(
f'{xlib.get_short_project_name()} - {self.head}', message)
# install the software
if OK:
# install the BLAST+ software
if self.app_code == xlib.get_blastplus_code():
# -- package_list = [(xlib.get_blastplus_conda_code(), 'last')]
package_list = [(xlib.get_blastplus_conda_code(), '2.9.0')]
dialog_log = gdialogs.DialogLog(
self, self.head,
xbioinfoapp.install_conda_package_list.__name__)
threading.Thread(target=self.wait_window,
args=(dialog_log, )).start()
threading.Thread(
target=xbioinfoapp.install_conda_package_list,
args=(self.app_code, self.app_name, package_list,
dialog_log,
lambda: dialog_log.enable_button_close())).start()
# install the DIAMOND software
elif self.app_code == xlib.get_diamond_code():
# -- package_list = [(xlib.get_diamond_conda_code(), 'last')]
package_list = [(xlib.get_diamond_conda_code(), '0.9.34')]
dialog_log = gdialogs.DialogLog(
self, self.head,
xbioinfoapp.install_conda_package_list.__name__)
threading.Thread(target=self.wait_window,
args=(dialog_log, )).start()
threading.Thread(
target=xbioinfoapp.install_conda_package_list,
args=(self.app_code, self.app_name, package_list,
dialog_log,
lambda: dialog_log.enable_button_close())).start()
# install the Entrez Direct software
elif self.app_code == xlib.get_entrez_direct_code():
package_list = [(xlib.get_entrez_direct_conda_code(), 'last')]
dialog_log = gdialogs.DialogLog(
self, self.head,
xbioinfoapp.install_conda_package_list.__name__)
threading.Thread(target=self.wait_window,
args=(dialog_log, )).start()
threading.Thread(
target=xbioinfoapp.install_conda_package_list,
args=(self.app_code, self.app_name, package_list,
dialog_log,
lambda: dialog_log.enable_button_close())).start()
# install the Miniconda3 software
elif self.app_code == xlib.get_miniconda3_code():
dialog_log = gdialogs.DialogLog(
self, self.head, xbioinfoapp.install_miniconda3.__name__)
threading.Thread(target=self.wait_window,
args=(dialog_log, )).start()
threading.Thread(
target=xbioinfoapp.install_miniconda3,
args=(dialog_log,
lambda: dialog_log.enable_button_close())).start()
# install R and analysis packages
elif self.app_code == xlib.get_r_code():
dialog_log = gdialogs.DialogLog(self, self.head,
xbioinfoapp.install_r.__name__)
threading.Thread(target=self.wait_window,
args=(dialog_log, )).start()
threading.Thread(
target=xbioinfoapp.install_r,
args=(dialog_log,
lambda: dialog_log.enable_button_close())).start()
# install the TransDecoder software
elif self.app_code == xlib.get_transdecoder_code():
package_list = [(xlib.get_transdecoder_conda_code(), 'last')]
dialog_log = gdialogs.DialogLog(
self, self.head,
xbioinfoapp.install_conda_package_list.__name__)
threading.Thread(target=self.wait_window,
args=(dialog_log, )).start()
threading.Thread(
target=xbioinfoapp.install_conda_package_list,
args=(self.app_code, self.app_name, package_list,
dialog_log,
lambda: dialog_log.enable_button_close())).start()
# close the form
if OK:
self.close()
def form_list_cluster_experiment_processes():
'''
List the processes of an experiment in the cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Logs - List experiment processes in the cluster')
# get the cluster name
print(xlib.get_separator())
if xec2.get_running_cluster_list(volume_creator_included=False) != []:
cluster_name = cinputs.input_cluster_name(volume_creator_included=False, help=True)
else:
print('WARNING: There is not any running cluster.')
OK = False
# create the SSH client connection
if OK:
(OK, error_list, ssh_client) = xssh.create_ssh_client_connection(cluster_name, 'master')
for error in error_list:
log.write('{0}\n'.format(error))
# get experiment identification
if OK:
experiment_id = cinputs.input_experiment_id(ssh_client, help=True)
if experiment_id == '':
print('WARNING: The cluster {0} has not experiment data.'.format(cluster_name))
OK = False
# get the result dataset list of the experiment
if OK:
command = 'cd {0}/{1}; for list in `ls`; do ls -ld $list | grep -v ^- > /dev/null && echo $list; done;'.format(xlib.get_cluster_result_dir(), experiment_id)
(OK, stdout, stderr) = xssh.execute_cluster_command(ssh_client, command)
if OK:
result_dataset_id_list = []
for line in stdout:
line = line.rstrip('\n')
if line != 'lost+found':
result_dataset_id_list.append(line)
# print the result dataset identification list of the experiment
if OK:
print(xlib.get_separator())
if result_dataset_id_list == []:
print('*** WARNING: There is not any result dataset of the experiment {0}.'.format(experiment_id))
else:
result_dataset_id_list.sort()
# set data width
result_dataset_width = 25
bioinfo_app_width = 25
# set line template
line_template = '{0:' + str(result_dataset_width) + '} {1:' + str(bioinfo_app_width) + '}'
# print header
print(line_template.format('Result dataset', 'Bioinfo app / Utility'))
print(line_template.format('=' * result_dataset_width, '=' * bioinfo_app_width))
# print detail lines
for result_dataset_id in result_dataset_id_list:
if result_dataset_id.startswith(xlib.get_bedtools_code()+'-'):
bioinfo_app_name = xlib.get_bedtools_name()
elif result_dataset_id.startswith(xlib.get_blastplus_code()+'-'):
bioinfo_app_name = xlib.get_blastplus_name()
elif result_dataset_id.startswith(xlib.get_bowtie2_code()+'-'):
bioinfo_app_name = xlib.get_bowtie2_name()
elif result_dataset_id.startswith(xlib.get_busco_code()+'-'):
bioinfo_app_name = xlib.get_busco_name()
elif result_dataset_id.startswith(xlib.get_cd_hit_code()+'-'):
bioinfo_app_name = xlib.get_cd_hit_est_name()
elif result_dataset_id.startswith(xlib.get_cd_hit_code()+'-'):
bioinfo_app_name = xlib.get_cd_hit_est_name()
elif result_dataset_id.startswith(xlib.get_detonate_code()+'-'):
bioinfo_app_name = xlib.get_detonate_name()
elif result_dataset_id.startswith(xlib.get_emboss_code()+'-'):
bioinfo_app_name = xlib.get_emboss_name()
elif result_dataset_id.startswith(xlib.get_fastqc_code()+'-'):
bioinfo_app_name = xlib.get_fastqc_name()
elif result_dataset_id.startswith(xlib.get_gmap_code()+'-'):
bioinfo_app_name = xlib.get_gmap_name()
elif result_dataset_id.startswith(xlib.get_gmap_gsnap_code()+'-'):
bioinfo_app_name = xlib.get_gmap_gsnap_name()
elif result_dataset_id.startswith(xlib.get_gzip_code()+'-'):
bioinfo_app_name = xlib.get_gzip_name()
elif result_dataset_id.startswith(xlib.get_insilico_read_normalization_code()+'-'):
bioinfo_app_name = xlib.get_insilico_read_normalization_name()
elif result_dataset_id.startswith(xlib.get_miniconda3_code()+'-'):
bioinfo_app_name = xlib.get_miniconda3_name()
elif result_dataset_id.startswith(xlib.get_ngshelper_code()+'-'):
bioinfo_app_name = xlib.get_ngshelper_name()
elif result_dataset_id.startswith(xlib.get_quast_code()+'-'):
bioinfo_app_name = xlib.get_quast_name()
elif result_dataset_id.startswith(xlib.get_r_code()+'-'):
bioinfo_app_name = xlib.get_r_name()
elif result_dataset_id.startswith(xlib.get_ref_eval_code()+'-'):
bioinfo_app_name = xlib.get_ref_eval_name()
elif result_dataset_id.startswith(xlib.get_rnaquast_code()+'-'):
bioinfo_app_name = xlib.get_rnaquast_name()
elif result_dataset_id.startswith(xlib.get_rsem_code()+'-'):
bioinfo_app_name = xlib.get_rsem_name()
elif result_dataset_id.startswith(xlib.get_rsem_eval_code()+'-'):
bioinfo_app_name = xlib.get_rsem_eval_name()
elif result_dataset_id.startswith(xlib.get_samtools_code()+'-'):
bioinfo_app_name = xlib.get_samtools_name()
elif result_dataset_id.startswith(xlib.get_soapdenovotrans_code()+'-'):
bioinfo_app_name = xlib.get_soapdenovotrans_name()
elif result_dataset_id.startswith(xlib.get_star_code()+'-'):
bioinfo_app_name = xlib.get_star_name()
elif result_dataset_id.startswith(xlib.get_transabyss_code()+'-'):
bioinfo_app_name = xlib.get_transabyss_name()
elif result_dataset_id.startswith(xlib.get_transcript_filter_code()+'-'):
bioinfo_app_name = xlib.get_transcript_filter_name()
elif result_dataset_id.startswith(xlib.get_transcriptome_blastx_code()+'-'):
bioinfo_app_name = xlib.get_transcriptome_blastx_name()
elif result_dataset_id.startswith(xlib.get_transrate_code()+'-'):
bioinfo_app_name = xlib.get_transrate_name()
elif result_dataset_id.startswith(xlib.get_trimmomatic_code()+'-'):
bioinfo_app_name = xlib.get_trimmomatic_name()
elif result_dataset_id.startswith(xlib.get_trinity_code()+'-'):
bioinfo_app_name = xlib.get_trinity_name()
else:
bioinfo_app_name = 'xxx'
print(line_template.format(result_dataset_id, bioinfo_app_name))
# close the SSH client connection
if OK:
xssh.close_ssh_client_connection(ssh_client)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def execute(self, event=None):
'''
Execute the list the result logs in the cluster.
'''
# validate inputs
OK = self.validate_inputs()
if not OK:
message = 'Some input values are not OK.'
tkinter.messagebox.showerror('{0} - {1}'.format(xlib.get_project_name(), self.head), message)
# get the run dictionary of the experiment
if OK:
# -- command = 'ls {0}/{1}'.format(xlib.get_cluster_result_dir(), self.wrapper_experiment_id.get())
command = 'cd {0}/{1}; for list in `ls`; do ls -ld $list | grep -v ^- > /dev/null && echo $list; done;'.format(xlib.get_cluster_result_dir(), self.wrapper_experiment_id.get())
(OK, stdout, stderr) = xssh.execute_cluster_command(self.ssh_client, command)
if OK:
result_dataset_dict = {}
for line in stdout:
line = line.rstrip('\n')
if line != 'lost+found':
result_dataset_id = line
try:
pattern = r'^(.+)\-(.+)\-(.+)$'
mo = re.search(pattern, result_dataset_id)
bioinfo_app_code = mo.group(1).strip()
yymmdd = mo.group(2)
hhmmss = mo.group(3)
date = '20{0}-{1}-{2}'.format(yymmdd[:2], yymmdd[2:4], yymmdd[4:])
time = '{0}:{1}:{2}'.format(hhmmss[:2], hhmmss[2:4], hhmmss[4:])
except:
bioinfo_app_code = 'xxx'
date = '0000-00-00'
time = '00:00:00'
if result_dataset_id.startswith(xlib.get_bedtools_code()+'-'):
bioinfo_app_name = xlib.get_bedtools_name()
elif result_dataset_id.startswith(xlib.get_blastplus_code()+'-'):
bioinfo_app_name = xlib.get_blastplus_name()
elif result_dataset_id.startswith(xlib.get_bowtie2_code()+'-'):
bioinfo_app_name = xlib.get_bowtie2_name()
elif result_dataset_id.startswith(xlib.get_busco_code()+'-'):
bioinfo_app_name = xlib.get_busco_name()
elif result_dataset_id.startswith(xlib.get_cd_hit_code()+'-'):
bioinfo_app_name = xlib.get_cd_hit_name()
elif result_dataset_id.startswith(xlib.get_cd_hit_est_code()+'-'):
bioinfo_app_name = xlib.get_cd_hit_est_name()
elif result_dataset_id.startswith(xlib.get_detonate_code()+'-'):
bioinfo_app_name = xlib.get_detonate_name()
elif result_dataset_id.startswith(xlib.get_emboss_code()+'-'):
bioinfo_app_name = xlib.get_emboss_name()
elif result_dataset_id.startswith(xlib.get_fastqc_code()+'-'):
bioinfo_app_name = xlib.get_fastqc_name()
elif result_dataset_id.startswith(xlib.get_gmap_code()+'-'):
bioinfo_app_name = xlib.get_gmap_name()
elif result_dataset_id.startswith(xlib.get_gmap_gsnap_code()+'-'):
bioinfo_app_name = xlib.get_gmap_gsnap_name()
elif result_dataset_id.startswith(xlib.get_gzip_code()+'-'):
bioinfo_app_name = xlib.get_gzip_name()
elif result_dataset_id.startswith(xlib.get_insilico_read_normalization_code()+'-'):
bioinfo_app_name = xlib.get_insilico_read_normalization_name()
elif result_dataset_id.startswith(xlib.get_miniconda3_code()+'-'):
bioinfo_app_name = xlib.get_miniconda3_name()
elif result_dataset_id.startswith(xlib.get_ngshelper_code()+'-'):
bioinfo_app_name = xlib.get_ngshelper_name()
elif result_dataset_id.startswith(xlib.get_quast_code()+'-'):
bioinfo_app_name = xlib.get_quast_name()
elif result_dataset_id.startswith(xlib.get_r_code()+'-'):
bioinfo_app_name = xlib.get_r_name()
elif result_dataset_id.startswith(xlib.get_ref_eval_code()+'-'):
bioinfo_app_name = xlib.get_ref_eval_name()
elif result_dataset_id.startswith(xlib.get_rnaquast_code()+'-'):
bioinfo_app_name = xlib.get_rnaquast_name()
elif result_dataset_id.startswith(xlib.get_rsem_code()+'-'):
bioinfo_app_name = xlib.get_rsem_name()
elif result_dataset_id.startswith(xlib.get_rsem_eval_code()+'-'):
bioinfo_app_name = xlib.get_rsem_eval_name()
elif result_dataset_id.startswith(xlib.get_samtools_code()+'-'):
bioinfo_app_name = xlib.get_samtools_name()
elif result_dataset_id.startswith(xlib.get_soapdenovotrans_code()+'-'):
bioinfo_app_name = xlib.get_soapdenovotrans_name()
elif result_dataset_id.startswith(xlib.get_star_code()+'-'):
bioinfo_app_name = xlib.get_star_name()
elif result_dataset_id.startswith(xlib.get_transabyss_code()+'-'):
bioinfo_app_name = xlib.get_transabyss_name()
elif result_dataset_id.startswith(xlib.get_transcript_filter_code()+'-'):
bioinfo_app_name = xlib.get_transcript_filter_name()
elif result_dataset_id.startswith(xlib.get_transcriptome_blastx_code()+'-'):
bioinfo_app_name = xlib.get_transcriptome_blastx_name()
elif result_dataset_id.startswith(xlib.get_transrate_code()+'-'):
bioinfo_app_name = xlib.get_transrate_name()
elif result_dataset_id.startswith(xlib.get_trimmomatic_code()+'-'):
bioinfo_app_name = xlib.get_trimmomatic_name()
elif result_dataset_id.startswith(xlib.get_trinity_code()+'-'):
bioinfo_app_name = xlib.get_trinity_name()
else:
bioinfo_app_name = 'xxx'
result_dataset_dict[result_dataset_id] = {'experiment_id': self.wrapper_experiment_id.get(), 'result_dataset_id': result_dataset_id, 'bioinfo_app': bioinfo_app_name, 'date': date, 'time': time}
# verify if there are any nodes running
if OK:
if result_dataset_dict == {}:
message = 'There is not any run.'
tkinter.messagebox.showwarning('{0} - {1}'.format(xlib.get_project_name(), self.head), message)
# build the data list
if OK:
data_list = ['experiment_id', 'result_dataset_id', 'bioinfo_app', 'date', 'time']
# build the data dictionary
if OK:
data_dict = {}
data_dict['experiment_id']= {'text': 'Experiment id. / Process', 'width': 200, 'aligment': 'left'}
data_dict['result_dataset_id'] = {'text': 'Result dataset', 'width': 200, 'aligment': 'left'}
data_dict['bioinfo_app'] = {'text': 'Bioinfo app / Utility', 'width': 200, 'aligment': 'left'}
data_dict['date'] = {'text': 'Date', 'width': 80, 'aligment': 'right'}
data_dict['time'] = {'text': 'Time', 'width': 80, 'aligment': 'right'}
# create the dialog Table to show the nodes running
if OK:
dialog_table = gdialogs.DialogTable(self, 'Experiment runs in {0}/{1}'.format(xlib.get_cluster_result_dir(), self.wrapper_experiment_id.get()), 400, 900, data_list, data_dict, result_dataset_dict, 'view_result_logs', [self.wrapper_cluster_name.get()])
self.wait_window(dialog_table)
# close the form
if OK:
self.close()
def form_install_bioinfo_app(app_code):
'''
Install the bioinfo application software in the cluster.
'''
# initialize the control variable
OK = True
# set the bioinfo application name
if app_code == xlib.get_blastplus_code():
app_name = xlib.get_blastplus_name()
elif app_code == xlib.get_diamond_code():
app_name = xlib.get_diamond_name()
elif app_code == xlib.get_entrez_direct_code():
app_name = xlib.get_entrez_direct_name()
elif app_code == xlib.get_miniconda3_code():
app_name = xlib.get_miniconda3_name()
elif app_code == xlib.get_r_code():
app_name = xlib.get_r_name()
elif app_code == xlib.get_transdecoder_code():
app_name = xlib.get_transdecoder_name()
# print the header
clib.clear_screen()
clib.print_headers_with_environment(f'{app_name} - Install software')
# confirm the software installation
print(xlib.get_separator())
if app_code == xlib.get_miniconda3_code():
OK = clib.confirm_action(
f'{app_name} (Conda infrastructure) is going to be installed. All Conda packages previously installed will be lost and they have to be reinstalled.'
)
elif app_code == xlib.get_r_code():
OK = clib.confirm_action(
f'{app_name} and analysis packages are going to be installed. The previous version will be lost, if it exists.'
)
else:
OK = clib.confirm_action(
f'The {app_name} Conda package is going to be installed. The previous version will be lost, if it exists.'
)
# install the software
if OK:
# install the BLAST+ software
if app_code == xlib.get_blastplus_code():
# -- package_code_list = [(xlib.get_blastplus_conda_code(), 'last')]
package_code_list = [(xlib.get_blastplus_conda_code(), '2.9.0')]
devstdout = xlib.DevStdOut(
xbioinfoapp.install_conda_package_list.__name__)
OK = xbioinfoapp.install_conda_package_list(app_code,
app_name,
package_code_list,
devstdout,
function=None)
# install the DIAMOND software
elif app_code == xlib.get_diamond_code():
# -- package_code_list = [(xlib.get_diamond_conda_code(), 'last')]
package_code_list = [(xlib.get_diamond_conda_code(), '0.9.34')]
devstdout = xlib.DevStdOut(
xbioinfoapp.install_conda_package_list.__name__)
OK = xbioinfoapp.install_conda_package_list(app_code,
app_name,
package_code_list,
devstdout,
function=None)
# install the Entrez Direct software
elif app_code == xlib.get_entrez_direct_code():
package_code_list = [(xlib.get_entrez_direct_conda_code(), 'last')]
devstdout = xlib.DevStdOut(
xbioinfoapp.install_conda_package_list.__name__)
OK = xbioinfoapp.install_conda_package_list(app_code,
app_name,
package_code_list,
devstdout,
function=None)
# install the Miniconda3 software
elif app_code == xlib.get_miniconda3_code():
devstdout = xlib.DevStdOut(xbioinfoapp.install_miniconda3.__name__)
OK = xbioinfoapp.install_miniconda3(devstdout, function=None)
# install R and analysis packages
elif app_code == xlib.get_r_code():
devstdout = xlib.DevStdOut(xbioinfoapp.install_r.__name__)
OK = xbioinfoapp.install_r(devstdout, function=None)
# install the TransDecoder software
elif app_code == xlib.get_transdecoder_code():
package_code_list = [(xlib.get_transdecoder_conda_code(), 'last')]
devstdout = xlib.DevStdOut(
xbioinfoapp.install_conda_package_list.__name__)
OK = xbioinfoapp.install_conda_package_list(app_code,
app_name,
package_code_list,
devstdout,
function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_list_cluster_experiment_processes():
'''
List the processes of an experiment in the cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment(
'Logs - List experiment processes in the cluster')
# get the cluster name
print(xlib.get_separator())
if xec2.get_running_cluster_list(only_environment_cluster=True,
volume_creator_included=False) != []:
cluster_name = cinputs.input_cluster_name(
volume_creator_included=False, help=True)
else:
print('WARNING: There is not any running cluster.')
OK = False
# create the SSH client connection
if OK:
(OK, error_list,
ssh_client) = xssh.create_ssh_client_connection(cluster_name)
for error in error_list:
print(error)
# get experiment identification
if OK:
experiment_id = cinputs.input_experiment_id(ssh_client, help=True)
if experiment_id == '':
print(
f'WARNING: The cluster {cluster_name} does not have experiment data.'
)
OK = False
# get the result dataset list of the experiment
if OK:
command = f'cd {xlib.get_cluster_result_dir()}/{experiment_id}; for list in `ls`; do ls -ld $list | grep -v ^- > /dev/null && echo $list; done;'
(OK, stdout, _) = xssh.execute_cluster_command(ssh_client, command)
if OK:
result_dataset_id_list = []
for line in stdout:
line = line.rstrip('\n')
if line != 'lost+found':
result_dataset_id_list.append(line)
# print the result dataset identification list of the experiment
if OK:
print(xlib.get_separator())
if result_dataset_id_list == []:
print(
f'*** WARNING: There is not any result dataset of the experiment {experiment_id}.'
)
else:
result_dataset_id_list.sort()
# set data width
result_dataset_width = 30
bioinfo_app_width = 25
# set line
line = '{0:' + str(result_dataset_width) + '} {1:' + str(
bioinfo_app_width) + '}'
# print header
print(line.format('Result dataset', 'Bioinfo app / Utility'))
print(
line.format('=' * result_dataset_width,
'=' * bioinfo_app_width))
# print detail lines
for result_dataset_id in result_dataset_id_list:
if result_dataset_id.startswith(xlib.get_bedtools_code() +
'-'):
bioinfo_app_name = xlib.get_bedtools_name()
elif result_dataset_id.startswith(xlib.get_blastplus_code() +
'-'):
bioinfo_app_name = xlib.get_blastplus_name()
elif result_dataset_id.startswith(xlib.get_bcftools_code() +
'-'):
bioinfo_app_name = xlib.get_bcftools_name()
elif result_dataset_id.startswith(xlib.get_bowtie2_code() +
'-'):
bioinfo_app_name = xlib.get_bowtie2_name()
elif result_dataset_id.startswith(xlib.get_busco_code() + '-'):
bioinfo_app_name = xlib.get_busco_name()
elif result_dataset_id.startswith(xlib.get_cd_hit_code() +
'-'):
bioinfo_app_name = xlib.get_cd_hit_name()
elif result_dataset_id.startswith(xlib.get_cd_hit_est_code() +
'-'):
bioinfo_app_name = xlib.get_cd_hit_est_name()
elif result_dataset_id.startswith(xlib.get_cuffdiff_code() +
'-'):
bioinfo_app_name = xlib.get_cuffdiff_name()
elif result_dataset_id.startswith(xlib.get_cufflinks_code() +
'-'):
bioinfo_app_name = xlib.get_cufflinks_name()
elif result_dataset_id.startswith(
xlib.get_cufflinks_cuffmerge_code() + '-'):
bioinfo_app_name = xlib.get_cufflinks_cuffmerge_name()
elif result_dataset_id.startswith(xlib.get_cuffnorm_code() +
'-'):
bioinfo_app_name = xlib.get_cuffnorm_name()
elif result_dataset_id.startswith(xlib.get_cuffquant_code() +
'-'):
bioinfo_app_name = xlib.get_cuffquant_name()
elif result_dataset_id.startswith(xlib.get_cutadapt_code() +
'-'):
bioinfo_app_name = xlib.get_cutadapt_name()
elif result_dataset_id.startswith(
xlib.get_ddradseq_simulation_code() + '-'):
bioinfo_app_name = xlib.get_ddradseq_simulation_name()
elif result_dataset_id.startswith(
xlib.get_ddradseqtools_code() + '-'):
bioinfo_app_name = xlib.get_ddradseqtools_name()
elif result_dataset_id.startswith(xlib.get_detonate_code() +
'-'):
bioinfo_app_name = xlib.get_detonate_name()
elif result_dataset_id.startswith(xlib.get_diamond_code() +
'-'):
bioinfo_app_name = xlib.get_diamond_name()
elif result_dataset_id.startswith(xlib.get_emboss_code() +
'-'):
bioinfo_app_name = xlib.get_emboss_name()
elif result_dataset_id.startswith(
xlib.get_entrez_direct_code() + '-'):
bioinfo_app_name = xlib.get_entrez_direct_name()
elif result_dataset_id.startswith(xlib.get_express_code() +
'-'):
bioinfo_app_name = xlib.get_express_name()
elif result_dataset_id.startswith(xlib.get_fastqc_code() +
'-'):
bioinfo_app_name = xlib.get_fastqc_name()
elif result_dataset_id.startswith(xlib.get_ggtrinity_code() +
'-'):
bioinfo_app_name = xlib.get_ggtrinity_name()
elif result_dataset_id.startswith(xlib.get_gmap_gsnap_code() +
'-'):
bioinfo_app_name = xlib.get_gmap_gsnap_name()
elif result_dataset_id.startswith(xlib.get_gmap_code() + '-'):
bioinfo_app_name = xlib.get_gmap_name()
elif result_dataset_id.startswith(xlib.get_gsnap_code() + '-'):
bioinfo_app_name = xlib.get_gsnap_name()
elif result_dataset_id.startswith(xlib.get_gzip_code() + '-'):
bioinfo_app_name = xlib.get_gzip_name()
elif result_dataset_id.startswith(xlib.get_hisat2_code() +
'-'):
bioinfo_app_name = xlib.get_hisat2_name()
elif result_dataset_id.startswith(xlib.get_htseq_code() + '-'):
bioinfo_app_name = xlib.get_htseq_name()
elif result_dataset_id.startswith(xlib.get_htseq_count_code() +
'-'):
bioinfo_app_name = xlib.get_htseq_count_name()
elif result_dataset_id.startswith(
xlib.get_insilico_read_normalization_code() + '-'):
bioinfo_app_name = xlib.get_insilico_read_normalization_name(
)
elif result_dataset_id.startswith(xlib.get_ipyrad_code() +
'-'):
bioinfo_app_name = xlib.get_ipyrad_name()
elif result_dataset_id.startswith(xlib.get_kallisto_code() +
'-'):
bioinfo_app_name = xlib.get_kallisto_name()
elif result_dataset_id.startswith(xlib.get_miniconda3_code() +
'-'):
bioinfo_app_name = xlib.get_miniconda3_name()
elif result_dataset_id.startswith(xlib.get_ngshelper_code() +
'-'):
bioinfo_app_name = xlib.get_ngshelper_name()
elif result_dataset_id.startswith(xlib.get_quast_code() + '-'):
bioinfo_app_name = xlib.get_quast_name()
elif result_dataset_id.startswith(xlib.get_r_code() + '-'):
bioinfo_app_name = xlib.get_r_name()
elif result_dataset_id.startswith(xlib.get_raddesigner_code() +
'-'):
bioinfo_app_name = xlib.get_raddesigner_name()
elif result_dataset_id.startswith(xlib.get_ref_eval_code() +
'-'):
bioinfo_app_name = xlib.get_ref_eval_name()
elif result_dataset_id.startswith(xlib.get_rnaquast_code() +
'-'):
bioinfo_app_name = xlib.get_rnaquast_name()
elif result_dataset_id.startswith(xlib.get_rsem_code() + '-'):
bioinfo_app_name = xlib.get_rsem_name()
elif result_dataset_id.startswith(xlib.get_rsem_eval_code() +
'-'):
bioinfo_app_name = xlib.get_rsem_eval_name()
elif result_dataset_id.startswith(xlib.get_rsitesearch_code() +
'-'):
bioinfo_app_name = xlib.get_rsitesearch_name()
elif result_dataset_id.startswith(xlib.get_samtools_code() +
'-'):
bioinfo_app_name = xlib.get_samtools_name()
elif result_dataset_id.startswith(xlib.get_soapdenovo2_code() +
'-'):
bioinfo_app_name = xlib.get_soapdenovo2_name()
elif result_dataset_id.startswith(
xlib.get_soapdenovotrans_code() + '-'):
bioinfo_app_name = xlib.get_soapdenovotrans_name()
elif result_dataset_id.startswith(xlib.get_star_code() + '-'):
bioinfo_app_name = xlib.get_star_name()
elif result_dataset_id.startswith(xlib.get_starcode_code() +
'-'):
bioinfo_app_name = xlib.get_starcode_name()
elif result_dataset_id.startswith(xlib.get_toa_code() + '-'):
bioinfo_app_name = xlib.get_toa_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_download_basic_data_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_basic_data_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_dicots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_dicots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_gene_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_gene_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_go_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_go_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_download_gymno_01_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_gymno_01_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_interpro_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_interpro_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_monocots_04_code() +
'-'):
bioinfo_app_name = xlib.get_toa_process_download_monocots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_taxonomy_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_taxonomy_name(
)
elif result_dataset_id.startswith(
xlib.
get_toa_process_gilist_viridiplantae_nucleotide_gi_code(
) + '-'):
bioinfo_app_name = xlib.get_toa_process_gilist_viridiplantae_nucleotide_gi_name(
)
elif result_dataset_id.startswith(
xlib.
get_toa_process_gilist_viridiplantae_protein_gi_code()
+ '-'):
bioinfo_app_name = xlib.get_toa_process_gilist_viridiplantae_protein_gi_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_basic_data_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_basic_data_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_dicots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_dicots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_gene_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_gene_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_load_go_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_go_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_load_gymno_01_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_gymno_01_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_interpro_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_interpro_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_monocots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_monocots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_merge_annotations_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_merge_annotations_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_nr_blastplus_db_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_nr_blastplus_db_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_nr_diamond_db_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_nr_diamond_db_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_nt_blastplus_db_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_nt_blastplus_db_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_pipeline_aminoacid_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_pipeline_aminoacid_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_pipeline_nucleotide_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_pipeline_nucleotide_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_dicots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_proteome_dicots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_gymno_01_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_proteome_gymno_01_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_monocots_04_code() +
'-'):
bioinfo_app_name = xlib.get_toa_process_proteome_monocots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_refseq_plant_code() +
'-'):
bioinfo_app_name = xlib.get_toa_process_proteome_refseq_plant_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_rebuild_toa_database_code() +
'-'):
bioinfo_app_name = xlib.get_get_toa_process_rebuild_toa_database_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_recreate_toa_database_code() +
'-'):
bioinfo_app_name = xlib.get_get_toa_process_recreate_toa_database_name(
)
elif result_dataset_id.startswith(xlib.get_tophat_code() +
'-'):
bioinfo_app_name = xlib.get_tophat_name()
elif result_dataset_id.startswith(xlib.get_transabyss_code() +
'-'):
bioinfo_app_name = xlib.get_transabyss_name()
elif result_dataset_id.startswith(
xlib.get_transcript_filter_code() + '-'):
bioinfo_app_name = xlib.get_transcript_filter_name()
elif result_dataset_id.startswith(
xlib.get_transcriptome_blastx_code() + '-'):
bioinfo_app_name = xlib.get_transcriptome_blastx_name()
elif result_dataset_id.startswith(
xlib.get_transdecoder_code() + '-'):
bioinfo_app_name = xlib.get_transdecoder_name()
elif result_dataset_id.startswith(xlib.get_transrate_code() +
'-'):
bioinfo_app_name = xlib.get_transrate_name()
elif result_dataset_id.startswith(xlib.get_trimmomatic_code() +
'-'):
bioinfo_app_name = xlib.get_trimmomatic_name()
elif result_dataset_id.startswith(xlib.get_trinity_code() +
'-'):
bioinfo_app_name = xlib.get_trinity_name()
elif result_dataset_id.startswith(
xlib.get_variant_calling_code() + '-'):
bioinfo_app_name = xlib.get_variant_calling_name()
elif result_dataset_id.startswith(xlib.get_vcftools_code() +
'-'):
bioinfo_app_name = xlib.get_vcftools_name()
elif result_dataset_id.startswith(
xlib.get_vcftools_perl_libraries_code() + '-'):
bioinfo_app_name = xlib.get_vcftools_perl_libraries_name()
elif result_dataset_id.startswith(xlib.get_vsearch_code() +
'-'):
bioinfo_app_name = xlib.get_vsearch_name()
else:
bioinfo_app_name = 'xxx'
print(line.format(result_dataset_id, bioinfo_app_name))
# close the SSH client connection
if OK:
xssh.close_ssh_client_connection(ssh_client)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_list_results_logs():
'''
List the processes of an experiment in the cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Logs - List result logs')
# get experiment identification
experiment_id = cinputs.input_experiment_id()
if experiment_id == '':
print('WARNING: There is not any experiment/process run.')
OK = False
# get the dictionary of TOA configuration.
if OK:
toa_config_dict = xtoa.get_toa_config_dict()
# get the result dataset list of the experiment
if OK:
experiment_dir = f'{toa_config_dict["RESULT_DIR"]}/{experiment_id}'
subdir_list = [
subdir for subdir in os.listdir(experiment_dir)
if os.path.isdir(os.path.join(experiment_dir, subdir))
]
result_dataset_id_list = []
for subdir in subdir_list:
result_dataset_id_list.append(subdir)
# print the result dataset identification list of the experiment
if OK:
print(xlib.get_separator())
if result_dataset_id_list == []:
print(
f'*** WARNING: There is not any result dataset of the experiment/process {experiment_id}.'
)
else:
result_dataset_id_list.sort()
# set data width
result_dataset_width = 25
bioinfo_app_width = 25
# set line template
line_template = '{0:' + str(
result_dataset_width) + '} {1:' + str(
bioinfo_app_width) + '}'
# print header
print(
line_template.format('Result dataset',
'Bioinfo app / Utility'))
print(
line_template.format('=' * result_dataset_width,
'=' * bioinfo_app_width))
# print detail lines
for result_dataset_id in result_dataset_id_list:
if result_dataset_id.startswith(xlib.get_blastplus_code() +
'-'):
bioinfo_app_name = xlib.get_blastplus_name()
elif result_dataset_id.startswith(xlib.get_diamond_code() +
'-'):
bioinfo_app_name = xlib.get_diamond_name()
elif result_dataset_id.startswith(
xlib.get_entrez_direct_code() + '-'):
bioinfo_app_name = xlib.get_entrez_direct_name()
elif result_dataset_id.startswith(xlib.get_miniconda3_code() +
'-'):
bioinfo_app_name = xlib.get_miniconda3_name()
elif result_dataset_id.startswith(xlib.get_r_code() + '-'):
bioinfo_app_name = xlib.get_r_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_download_basic_data_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_basic_data_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_dicots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_dicots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_gene_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_gene_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_go_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_go_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_download_gymno_01_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_gymno_01_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_interpro_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_interpro_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_monocots_04_code() +
'-'):
bioinfo_app_name = xlib.get_toa_process_download_monocots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_taxonomy_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_taxonomy_name(
)
elif result_dataset_id.startswith(
xlib.
get_toa_process_gilist_viridiplantae_nucleotide_gi_code(
) + '-'):
bioinfo_app_name = xlib.get_toa_process_gilist_viridiplantae_nucleotide_gi_name(
)
elif result_dataset_id.startswith(
xlib.
get_toa_process_gilist_viridiplantae_protein_gi_code()
+ '-'):
bioinfo_app_name = xlib.get_toa_process_gilist_viridiplantae_protein_gi_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_basic_data_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_basic_data_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_dicots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_dicots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_gene_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_gene_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_load_go_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_go_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_load_gymno_01_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_gymno_01_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_interpro_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_interpro_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_monocots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_monocots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_merge_annotations_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_merge_annotations_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_nr_blastplus_db_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_nr_blastplus_db_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_nr_diamond_db_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_nr_diamond_db_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_nt_blastplus_db_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_nt_blastplus_db_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_pipeline_aminoacid_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_pipeline_aminoacid_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_pipeline_nucleotide_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_pipeline_nucleotide_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_dicots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_proteome_dicots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_gymno_01_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_proteome_gymno_01_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_monocots_04_code() +
'-'):
bioinfo_app_name = xlib.get_toa_process_proteome_monocots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_refseq_plant_code() +
'-'):
bioinfo_app_name = xlib.get_toa_process_proteome_refseq_plant_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_rebuild_toa_database_code() +
'-'):
bioinfo_app_name = xlib.get_get_toa_process_rebuild_toa_database_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_recreate_toa_database_code() +
'-'):
bioinfo_app_name = xlib.get_get_toa_process_recreate_toa_database_name(
)
elif result_dataset_id.startswith(
xlib.get_transdecoder_code() + '-'):
bioinfo_app_name = xlib.get_transdecoder_name()
else:
bioinfo_app_name = 'xxx'
print(line_template.format(result_dataset_id,
bioinfo_app_name))
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')