def form_run_pipeline_process(pipeline_type):
'''
Run a pipeline process with the parameters in the corresponding config file.
'''
# initialize the control variable
OK = True
# set the pipeline name
if pipeline_type == xlib.get_toa_process_pipeline_nucleotide_code():
name = xlib.get_toa_process_pipeline_nucleotide_name()
elif pipeline_type == xlib.get_toa_process_pipeline_aminoacid_code():
name = xlib.get_toa_process_pipeline_aminoacid_name()
elif pipeline_type == xlib.get_toa_process_merge_annotations_code():
name = xlib.get_toa_process_merge_annotations_name()
# print the header
clib.clear_screen()
clib.print_headers_with_environment(f'{name} - Run process')
# confirm the process run
if OK:
print(xlib.get_separator())
OK = clib.confirm_action(f'The {name} process is going to be run.')
# run the process
if OK:
if pipeline_type == xlib.get_toa_process_pipeline_nucleotide_code():
devstdout = xlib.DevStdOut(xtoa.run_pipeline_process.__name__)
OK = xtoa.run_pipeline_process(pipeline_type,
devstdout,
function=None)
elif pipeline_type == xlib.get_toa_process_pipeline_aminoacid_code():
devstdout = xlib.DevStdOut(xtoa.run_pipeline_process.__name__)
OK = xtoa.run_pipeline_process(pipeline_type,
devstdout,
function=None)
elif pipeline_type == xlib.get_toa_process_merge_annotations_code():
devstdout = xlib.DevStdOut(
xtoa.run_annotation_merger_process.__name__)
OK = xtoa.run_annotation_merger_process(devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_manage_toa_database(process_type):
'''
Manage the TOA database.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
if process_type == xlib.get_toa_type_recreate():
clib.print_headers_with_environment(
f'{xlib.get_toa_name()} - Recreate database')
elif process_type == xlib.get_toa_type_rebuild():
clib.print_headers_with_environment(
f'{xlib.get_toa_name()} - Rebuild database')
# confirm the process run
if OK:
print(xlib.get_separator())
OK = clib.confirm_action(
f'The {xlib.get_toa_name()} database is going to be {process_type}.'
)
# run the process
if OK:
devstdout = xlib.DevStdOut(xtoa.manage_toa_database.__name__)
OK = xtoa.manage_toa_database(process_type, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_restart_cluster():
'''
Restart a cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Cluster operation - Restart cluster')
# get the cluster name
print(xlib.get_separator())
if xec2.get_running_cluster_list(volume_creator_included=False) == []:
print('WARNING: There is not any running cluster.')
OK = False
else:
cluster_name = cinputs.input_cluster_name(volume_creator_included=False, help=True)
# confirm the restarting of the cluster
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The cluster is going to be restarted.')
# stop the cluster
if OK:
devstdout = xlib.DevStdOut(xcluster.restart_cluster.__name__)
OK = xcluster.restart_cluster(cluster_name, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_remove_volume():
'''
Remove a volume in the current zone.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Volume operation - Remove volume')
# get current zone name
zone_name = xconfiguration.get_current_zone_name()
# get the volume name
print(xlib.get_separator())
volume_name = cinputs.input_volume_name(zone_name, template_name='', help=True, help_type='created')
# confirm the removal of the volume
print(xlib.get_separator())
OK = clib.confirm_action('The volume is going to be removed.')
# remove the volume
if OK:
devstdout = xlib.DevStdOut(xvolume.remove_volume.__name__)
OK = xvolume.remove_volume(volume_name, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_show_cluster_composing():
'''
Show cluster information of every node: OS, CPU number and memory.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Cluster operation - Show cluster composing')
# get the cluster name
print(xlib.get_separator())
if xec2.get_running_cluster_list(volume_creator_included=False) == []:
print('WARNING: There is not any running cluster.')
OK = False
else:
cluster_name = cinputs.input_cluster_name(volume_creator_included=False, help=True)
# show the status of batch jobs
if OK:
devstdout = xlib.DevStdOut(xcluster.show_cluster_composing.__name__)
xcluster.show_cluster_composing(cluster_name, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_kill_batch_job():
'''
Kill a batch job in the cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Cluster operation - Kill batch job')
# get the cluster name, experiment identification, read dataset identification and the file pattern
print(xlib.get_separator())
if xec2.get_running_cluster_list(volume_creator_included=False) == []:
print('WARNING: There is not any running cluster.')
OK = False
else:
cluster_name = cinputs.input_cluster_name(volume_creator_included=False, help=True)
# 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:
print(error)
# get the batch job identificaction
if OK:
batch_job_id = cinputs.input_batch_job_id(ssh_client, help=True)
if batch_job_id == '':
print('WARNING: There is not any batch job.')
OK = False
# confirm the kill of the batch job
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The batch job {0} is going to be killed.'.format(batch_job_id))
# kill the batch job
if OK:
devstdout = xlib.DevStdOut(xcluster.kill_batch_job.__name__)
xcluster.kill_batch_job(cluster_name, batch_job_id, devstdout, function=None)
# 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_delink_volume_from_template():
'''
Delink a volume from a cluster template
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Configuration - Delink volume in a cluster template')
# get current zone name
zone_name = xconfiguration.get_current_zone_name()
# get the template name and the volume name
print(xlib.get_separator())
template_name = cinputs.input_template_name(volume_creator_included=False, help=True, is_all_possible=True)
volume_name = cinputs.input_volume_name(zone_name, template_name, help=True, help_type='linked')
# verify there is some volume linked to the cluster template
if volume_name == '':
print(xlib.get_separator())
print('*** WARNING: There is not any volume linked to the cluster template.')
OK = False
# confirm the exclusion of the volume
if OK:
print(xlib.get_separator())
if template_name == 'all':
OK = clib.confirm_action('The volume {0} is going to be delinked from every template.'.format(volume_name))
else:
OK = clib.confirm_action('The volume {0} is going to be delinked from the template {0}.'.format(volume_name, template_name))
# delink a volume in a cluster template
if OK:
print(xlib.get_separator())
print('The volume {0} is being delinked from the cluster template {1}.'.format(volume_name, template_name))
devstdout = xlib.DevStdOut(xconfiguration.delink_volume_from_template.__name__)
(OK, error_list) = xconfiguration.delink_volume_from_template(template_name, volume_name, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_restart_pipeline_process(pipeline_type):
'''
Restart a pipeline process from the last step ended OK.
'''
# initialize the control variable
OK = True
# set the pipeline name
if pipeline_type == xlib.get_toa_process_pipeline_nucleotide_code():
name = xlib.get_toa_process_pipeline_nucleotide_name()
elif pipeline_type == xlib.get_toa_process_pipeline_aminoacid_code():
name = xlib.get_toa_process_pipeline_aminoacid_name()
# print the header
clib.clear_screen()
clib.print_headers_with_environment(f'{name} - Run process')
# get the pipeline dataset identification
app_list = [pipeline_type]
pipeline_dataset_id = cinputs.input_result_dataset_id(
xlib.get_toa_result_pipeline_dir(), app_list)
if pipeline_dataset_id == '':
print(f'WARNING: There are not any {pipeline_type} result datasets.')
OK = False
# confirm the process run
if OK:
print(xlib.get_separator())
OK = clib.confirm_action(f'The {name} process is going to be run.')
# run the process
if OK:
devstdout = xlib.DevStdOut(xtoa.restart_pipeline_process.__name__)
OK = xtoa.restart_pipeline_process(pipeline_type,
pipeline_dataset_id,
devstdout,
function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_mount_volume():
'''
Mount a volume in a node.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Volume operation - Mount volume in a node')
# get current zone name
zone_name = xconfiguration.get_current_zone_name()
# get the cluster name and node 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)
node_name = cinputs.input_node_name(cluster_name, new=False, is_master_valid=True, help=True)
else:
print('WARNING: There is not any running cluster.')
OK = False
# get the volume name, AWS device file and directory path
if OK:
volume_name = cinputs.input_volume_name(zone_name, template_name='', help=True, help_type='created')
aws_device_file = cinputs.input_device_file(node_name, volume_name)
mounting_path = cinputs.input_mounting_path(node_name, aws_device_file)
# confirm the mounting of the volume
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The volume is going to be mounted.')
# mount the volume in the node
if OK:
devstdout = xlib.DevStdOut(xvolume.mount_volume.__name__)
xvolume.mount_volume(cluster_name, node_name, volume_name, aws_device_file, mounting_path, devstdout, function=None, is_menu_call=True)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_list_clusters():
'''
List clusters.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Cluster operation - List clusters')
# list clusters
devstdout = xlib.DevStdOut(xcluster.list_clusters.__name__)
OK = xcluster.list_clusters(devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_terminate_cluster(force):
'''
Terminate a cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
if not force:
clib.print_headers_with_environment('Cluster operation - Terminate cluster')
else:
clib.print_headers_with_environment('Cluster operation - Force termination of a cluster')
# get the cluster name that must be terminated
print(xlib.get_separator())
if not force:
if xec2.get_running_cluster_list(volume_creator_included=False) == []:
print('WARNING: There is not any running cluster.')
OK = False
else:
cluster_name = cinputs.input_cluster_name(volume_creator_included=False, help=True)
else:
cluster_name = cinputs.input_template_name(volume_creator_included=False, help=False, is_all_possible=False)
# confirm the termination of the cluster
if OK:
print(xlib.get_separator())
if not force:
OK = clib.confirm_action('The cluster is going to be terminated.')
else:
OK = clib.confirm_action('The cluster is going to be forced to terminate.')
# terminate the cluster
if OK:
devstdout = xlib.DevStdOut(xcluster.terminate_cluster.__name__)
OK = xcluster.terminate_cluster(cluster_name, force, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_review_volume_links():
'''
Review linked volumes of cluster templates in order to remove linked volumes
that do not currently exist.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Configuration - Review volumes linked to cluster templates')
# get current zone name
zone_name = xconfiguration.get_current_zone_name()
# get the NGScloud confign file
ngscloud_config_file = xconfiguration.get_ngscloud_config_file()
# verify if there are any volumes linked
if xconfiguration.get_volumes_dict() == {}:
print(xlib.get_separator())
print('WARNING: There is not any volume linked.')
OK = False
# confirm the review of volumes links
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The file {0} is going to be reviewed in order to remove volumes linked which are not currently created in the zone {1}.'.format(ngscloud_config_file, zone_name))
# review volumen link
if OK:
devstdout = xlib.DevStdOut(xconfiguration.review_volume_links.__name__)
(OK, error_list) = xconfiguration.review_volume_links(zone_name, devstdout, function=None)
# show continuation message or exit of application
print(xlib.get_separator())
if not OK and error_list != []:
raise xlib.ProgramException('C001')
else:
input('Press [Intro] to continue ...')
def form_create_volume():
'''
Create a volume in the current zone.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Volume operation - Create volume')
# get current zone name
zone_name = xconfiguration.get_current_zone_name()
# show sites related to EBS volumes
print(xlib.get_separator())
print('You can consult the characteristics of the EBS volumes in:')
print(' https://aws.amazon.com/ebs/details/')
print('and the EBS pricing is detailed in:')
print(' https://aws.amazon.com/ebs/pricing/')
# get the cluster name, node name, volume name, volume type and volume size
print(xlib.get_separator())
volume_name = cinputs.input_volume_name(zone_name, template_name='', help=False, help_type='created')
volume_type = cinputs.input_volume_type()
volume_size = cinputs.input_volume_size(volume_type)
terminate_indicator = cinputs.input_terminate_indicator()
# confirm the creation of the volume
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The volume is going to be created.')
# create the volume
if OK:
devstdout = xlib.DevStdOut(xvolume.create_volume.__name__)
OK = xvolume.create_volume(volume_name, volume_type, volume_size, terminate_indicator, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_create_cluster():
'''
Create a cluster from a template name.
'''
# initialize the control variable
OK = True
# initialize the state variables
master_state_code = ''
master_state_name = ''
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Cluster operation - Create cluster')
# show sites related to EBS volumes
print(xlib.get_separator())
print('You can consult the characteristics of the EC2 intance types in:')
print(' https://aws.amazon.com/ec2/instance-types/')
print('and the EC2 pricing is detailed in:')
print(' https://aws.amazon.com/ec2/pricing/')
print()
# get the template name and set the cluster name
print(xlib.get_separator())
template_name = cinputs.input_template_name(volume_creator_included=False, help=True, is_all_possible=False)
cluster_name = template_name
# confirm the creation of the cluster
print(xlib.get_separator())
OK = clib.confirm_action('The cluster is going to be created.')
# create the cluster
if OK:
devstdout = xlib.DevStdOut(xcluster.create_cluster.__name__)
(OK, master_state_code, master_state_name) = xcluster.create_cluster(template_name, cluster_name, devstdout, function=None, is_menu_call=True)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_add_node():
'''
Add a node in a cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Node operation - Add node in a cluster')
# get the cluster name and node 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)
if len(xec2.get_cluster_node_list(cluster_name)) >= xec2.get_max_node_number():
print('WARNING: The maximum number ({0}) of instances is already running.'.format(xec2.get_max_node_number()))
OK = False
else:
node_name = cinputs.input_node_name(cluster_name, new=True, is_master_valid=False, help=True)
else:
print('WARNING: There is not any running cluster.')
OK = False
# confirm the addition of the node in the cluster
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The node is going to be added.')
# add node in cluster
if OK:
devstdout = xlib.DevStdOut(xnode.add_node.__name__)
xnode.add_node(cluster_name, node_name, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_remove_node():
'''
Remove a node in a cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Node operation - Remove node in a cluster')
# get the cluster name and node 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)
node_name = cinputs.input_node_name(cluster_name, new=False, is_master_valid=False, help=True)
if node_name == []:
print('WARNING: There is not any running node besides the master.')
OK = False
else:
print('WARNING: There is not any running cluster.')
OK = False
# confirm the removal of the node in the cluster
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The node is going to be removed.')
# remove node
if OK:
devstdout = xlib.DevStdOut(xnode.remove_node.__name__)
xnode.remove_node(cluster_name, node_name, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_terminate_volume_creator():
'''
Terminate de volume creator of the current zone.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Volume operation - Terminate volume creator')
# confirm the termination of the volume creator
print(xlib.get_separator())
OK = clib.confirm_action('The volume creator is going to be terminated.')
# terminate the volume creator
if OK:
devstdout = xlib.DevStdOut(xcluster.terminate_cluster.__name__)
xcluster.terminate_cluster(xlib.get_volume_creator_name(), True, devstdout, function=None, is_menu_call=False)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_manage_genomic_database(process_type, genomic_database):
'''
Manage processes of genomic database.
'''
# initialize the control variable
OK = True
# set the genomica database name
if genomic_database == xlib.get_toa_data_basic_data_code():
name = xlib.get_toa_data_basic_data_name()
elif genomic_database == xlib.get_toa_data_gymno_01_code():
name = xlib.get_toa_data_gymno_01_name()
elif genomic_database == xlib.get_toa_data_dicots_04_code():
name = xlib.get_toa_data_dicots_04_name()
elif genomic_database == xlib.get_toa_data_monocots_04_code():
name = xlib.get_toa_data_monocots_04_name()
elif genomic_database == xlib.get_toa_data_refseq_plant_code():
name = xlib.get_toa_data_refseq_plant_name()
elif genomic_database == xlib.get_toa_data_taxonomy_code():
name = xlib.get_toa_data_taxonomy_name()
elif genomic_database == xlib.get_toa_data_nt_code():
name = xlib.get_toa_data_nt_name()
elif genomic_database == xlib.get_toa_data_viridiplantae_nucleotide_gi_code(
):
name = xlib.get_toa_data_viridiplantae_nucleotide_gi_name()
elif genomic_database == xlib.get_toa_data_nr_code():
name = xlib.get_toa_data_nr_name()
elif genomic_database == xlib.get_toa_data_viridiplantae_protein_gi_code():
name = xlib.get_toa_data_viridiplantae_protein_gi_name()
elif genomic_database == xlib.get_toa_data_gene_code():
name = xlib.get_toa_data_gene_name()
elif genomic_database == xlib.get_toa_data_interpro_code():
name = xlib.get_toa_data_interpro_name()
elif genomic_database == xlib.get_toa_data_go_code():
name = xlib.get_toa_data_go_name()
# print the header
clib.clear_screen()
if process_type == xlib.get_toa_type_build_blastplus_db():
clib.print_headers_with_environment(f'Build {name} for BLAST+')
elif process_type == xlib.get_toa_type_build_diamond_db():
clib.print_headers_with_environment(f'Build {name} for DIAMOND')
elif process_type == xlib.get_toa_type_build_gilist():
clib.print_headers_with_environment(f'Build {name}')
elif process_type == xlib.get_toa_type_build_proteome():
clib.print_headers_with_environment(f'Build {name} proteome')
elif process_type == xlib.get_toa_type_download_data():
clib.print_headers_with_environment(
f'Download {name} functional annotations')
elif process_type == xlib.get_toa_type_load_data():
clib.print_headers_with_environment(
f'Load {name} data in {xlib.get_toa_name()} database')
print(xlib.get_separator())
# confirm the process run
if OK:
OK = clib.confirm_action(f'The {name} process is going to be run.')
# run the process
if OK:
devstdout = xlib.DevStdOut(xtoa.manage_genomic_database.__name__)
OK = xtoa.manage_genomic_database(process_type,
genomic_database,
devstdout,
function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def main(argv):
'''
Main line of the program.
'''
# verify the operating system.
if not sys.platform.startswith('linux') and not sys.platform.startswith(
'darwin') and not sys.platform.startswith(
'win32') and not sys.platform.startswith('cygwin'):
print('*** ERROR: The {1} OS is not supported.'.format(sys.platform))
sys.exit(1)
# verify the Python version.
if sys.version_info[0] == 3 and sys.version_info[1] >= 5:
pass
else:
print('A Python version equal or greater than 3.5 is required.')
sys.exit(1)
# verify if Boto3 is set up
try:
import boto3
except:
print('*** ERROR: The library boto3 is not installed.')
print('Please, review how to set up Boto3 in the manual.')
sys.exit(1)
# verify if Paramiko is set up
try:
import paramiko
except:
print('*** ERROR: The library paramiko is not installed.')
print('Please, review how to set up Paramiko in the manual.')
sys.exit(1)
# verify if Paramiko is set up
try:
import paramiko
except:
print('*** ERROR: The library paramiko is not installed.')
print('Please, review how to set up Paramiko in the manual.')
sys.exit(1)
# get and verify the options
parser = build_parser()
(options, args) = parser.parse_args()
verify_options(options)
# verify if the required graphical libraries are setup
if options.mode == 'gui' or options.mode is None:
# verify if the library PIL.Image is set up
try:
import tkinter
except:
print('*** ERROR: The library tkinter is not installed.')
print('Please, review how to set up Tkinter in the manual.')
sys.exit(1)
# verify if the library PIL.Image is set up
try:
import PIL.Image
except:
print('*** ERROR: The library PIL.Image is not installed.')
print('Please, review how to set up PIL.Image in the manual.')
sys.exit(1)
# verify if the library PIL.ImageTk is set up
try:
import PIL.ImageTk
except:
print('*** ERROR: The library PIL.ImageTk is not installed.')
print('Please, review how to set up PIL.ImageTk in the manual.')
sys.exit(1)
# import required application libraries
import ccloud
import cmenu
import gmain
import xlib
# verify if StarCluster is set up
command = '{0} --version'.format(xlib.get_starcluster())
devstdout = xlib.DevStdOut('starcluster_version', print_stdout=False)
rc = xlib.run_command(command, devstdout)
if rc != 0:
print(
'*** ERROR: The cluster-computing toolkit StarCluster 0.95.6 is not installed or excecution permissions have not set.'
)
print('Please, review how to set up in the manual.')
sys.exit(1)
else:
with open(devstdout.get_log_file(), 'r') as log_command:
version_found = False
for line in log_command:
if line.startswith('0.95.6'):
version_found = True
if not version_found:
print(
'*** ERROR: The cluster-computing toolkit StarCluster 0.95.6 is not installed or excecution permissions have not set.'
)
print('Please, review how to set up in the manual.')
sys.exit(1)
# start the user interface depending on the mode
if options.mode == 'gui' or options.mode is None:
main = gmain.Main()
main.mainloop()
else:
ccloud.form_set_environment()
cmenu.build_menu_main()
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 ...')