Global section

NG6 includes a workflow management system coming with a WEB server.

Property Default Description
makeflow /usr/bin/makeflow The path to the makeflow executable.
batch_system_type local The name of the batch system type to use. Supported batch systems are:
  • local
  • condor
  • sge
  • moab
  • cluster
  • wq
  • hadoop
  • mpi-queue
batch_options - Those options will be added to all submitted batch files.
limit_submission 100 The limit number of jobs submitted in parallel.
server_socket_host 127.0.0.1 The WEB address to use to run the workflow management system server.
server_socket_port 8080 The WEB server socket port to use to run the workflow management system server.
date_format %d/%m/%Y The default date format to use in the application for date parameters. This must be a date format string.

Email section

NG6 offers the possibility to send emails to the users at the end of a workflow execution. This can be done by editing the email section of the application.properties file.

To access this functionality, smtp_server, smtp_port, from_address and from_password are required parameters. The values subject and message can be globaly set from the NG6 configuration file or can be set within a workflow by using respectivly the self.set_subject() and self.set_message() methods.

Property Default Description
smtp_server - The smtp server used to send the email.
smtp_port - The smtp server port number.
from_address - Email used as "from" while sending the email.
from_password - The password associated with from_address on the smtp server.
subject - The subject of the mail. This value will be used for all workflow. It can be overloaded within the workflow implementation using self.set_subject("subject")
message - The mail content. This value will be used for all workflow. It can be overloaded within the workflow implementation using self.set_message("message")

Database section

The database section allows to configure the connection to a MYSQL database. Those connection information will be used to install all NG6 database.

Property Default Description
host localhost The hostname where the database is located.
dbname - The name of a database where to install ng6 database.
user - A user with read and write access to dbname.
passwd - Password for the user in dbname.

Storage section

This section configure the paths used by all workflows.

Property Default Description
log_file <path>/ng6.log The path to the log file for workflows execution. Errors and logs will be stored in this file.
save_directory <path>/save The path to the save directory. The save directory is the location where all ng6 data will be stored.
work_directory <path>/work The path to the work directory. This is the location where workflows will write results. If using a cluster, this location should be accessible by all cluster nodes.
tmp_directory <path>/tmp The path to the tmp directory. If using a cluster, this location should be accessible by all cluster nodes.

Softwares section

While retrieving a path from a workflow using self.get_exec_path('my_software'), NG6 will first look in the sofwares section of the configuration file to get the full path of 'my_software'. If this one is nout found, NG6 will then search within the workflows/bin/ directory. Finally, NG6 search in the system PATH variable to find the right path. 

# where could be find binaries
[softwares]
cutadapt = /path/to/cutadapt

Components section

In a production environment, it can be useful to custom DMS options for each components. To do so, within the components section in the jflow configuration file, add a line following the schema: [component_name].batch_options = [options].

[components]
BWAIndex.batch_options = -l mem=1G -l h_vmem=1G -q myflowq
BWAmem.batch_options = -l mem=10G -l h_vmem=10G -q myflow2q

Workflows section

Each workflow has a default group. In this section you can set a group name for each one of your workflow, thus while using the availablewf() plugin, you will be able to specify which group of workflow you want to get. You can set the group of a workflow by adding a line of the following schema : [workflow_classname].group = [group_name].

[workflows]
QuickStart.group = tutorial

Ressources section

In a production environment, it can be useful to set an ensemble of variables, such as path to databanks, for multiple workflows. Thus, NG6 gives access to ressources settled within the application.properties file. All the values settled within this section are then accessible from any Component or Workflow through the get_resource() class method.

[resources]
ecoli_db = /path/to/ecoli536
phix_db = /path/to/phi.fa
...