partekflow

master branch:

Module Description - What the module does and why it is useful
Setup - The basics of getting started with partekflow
- What partekflow affects
- Beginning with partekflow
Usage - Configuration options and additional functionality
Reference - An under-the-hood peek at what the module is doing and how
Limitations - OS compatibility, etc.
Development - Guide for contributing to the module

Module Description

The partekflow module installs, configures, and manages Partek Flow software package and service. Partek Flow is "designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing" that includes a web interface for creation and utilization of custom pipelines. http://www.partek.com/partekflow

Setup

What partekflow affects

User and Group: flow
Group: flowuser
RPM GPG Key: /etc/pki/rpm-gpg/partek-public.key
Yumrepos for accessing partek flow RPM repositories. The stable repositories are enabled while the unstable ones are not.
Package: partekflow
File: /etc/partekflow.conf
Catalina temp directory location
Service: partekflowd

Beginning with partekflow

include partekflow should be all that is needed to install, configure and start the partekflowd service. One can also pass parameters in to change the configuration:

class { 'partekflow':
    config_catalina_tmpdir => '/home/flow/partek_flow/temp',
}

Usage

All parameters are passed to the main class via either puppet code or hiera. The other classes should not be called directly. Some usage examples are presented below.

Install and startup partekflowd service

include partekflow

Change the location of the CATALINA_TMPDIR setting in /etc/partekflow.conf

class { 'partekflow':
  config_catalina_tmpdir => '/home/flow/partek_flow/temp',
}

or via hiera:

---
partekflow::config_catalina_tmpdir: '/home/flow/partek_flow/temp'

To use a different template for the partekflow.conf file

class { 'partekflow':
  config_template => 'module_name/path/to/template.erb',
}

To disable the stable repsitory files but still have them present in /etc/yum.repos.d/

class { 'partekflow':
  yumrepo_ensure_stable  => true,
  yumrepo_enabled_stable => false,
}

To use a local repository mirror instead of the Partek repositories

class { 'partekflow':
  yumrepo_baseurl_server       => 'http://yum.example.com',
  yumrepo_baseurl_stablepath   => '/path/to/stable',
  yumrepo_baseurl_unstablepath => '/path/to/unstable',
}

To remove the unstable /etc/yum.repos.d/ files

class { 'partekflow':
  yumrepo_ensure_unstable => false,
}

Reference

Generated puppet strings documentation with examples is available from https://millerjl1701.github.io/millerjl1701-partekflow/.

It's also included in the docs/ folder as simple html pages.

Classes

Public Classes

partekflow: Main class. Contains or calls all other classes or defines.

Private Classes

partekflow::config: Handles configuration of the service.
partekflow::install: Handles the installation of the software.
partekflow::service: Manages the partekflowd service.

Parameters

The partekflow::init class has the following parameters:

Stdlib::Absolutepath        $config_catalina_tmpdir       = '/opt/partek_flow/temp',
Stdlib::Absolutepath        $config_file                  = '/etc/partekflow.conf',
Stdlib::Absolutepath        $config_installdir            = '/opt/partek_flow',
String                      $config_template              = 'partekflow/partekflow.conf.erb',
String                      $package_ensure               = 'present',
String                      $package_name                 = 'partekflow',
Boolean                     $service_enable               = true,
Enum['running', 'stopped']  $service_ensure               = 'running',
String                      $service_name                 = 'partekflowd',
String                      $user_comment                 = 'Partek Flow daemon',
Enum['present', 'absent']   $user_ensure                  = 'present',
Integer[1, 999]             $user_gid                     = 495,
String                      $user_groupname               = 'flowuser',
Integer[1, 999]             $user_groupname_gid           = 494,
Stdlib::Absolutepath        $user_home                    = '/home/flow',
Boolean                     $user_managehome              = true,
String                      $user_name                    = 'flow',
Stdlib::Absolutepath        $user_shell                   = '/bin/sh',
Integer[1, 999]             $user_uid                     = 495,
Optional[Stdlib::Httpurl]   $yumrepo_baseurl_server       = undef,
Optional[String]            $yumrepo_baseurl_stablepath   = undef,
Optional[String]            $yumrepo_baseurl_unstablepath = undef,
Optional[Boolean]           $yumrepo_enabled_stable       = undef,
Optional[Boolean]           $yumrepo_enabled_unstable     = undef,
Optional[Boolean]           $yumrepo_ensure_stable        = undef,
Optional[Boolean]           $yumrepo_ensure_unstable      = undef,
Optional[Boolean]           $yumrepo_manage               = undef

Limitations

This module is written to work with Puppet 4.7 or higher. Hiera 5 data is embedded within the module as well for Puppet 4.9 or higher. The module depends on Puppet 4 data types provided by puppetlabs-stdlib as well as the treydock-gpg_key module.

Originally written for CentOS 6/7 systems, it could work on other osfamily RedHat distributions. While Partek Flow supports installation on Debian based distributions, this module does not at this time.

This module was written to reflect initial installation and configuration documentation provided by Partek. This is not an all inclusive module as there are configuration tasks that need to be done via the web UI to configure portions of the application. If you find some configuration option would be helpful for maintaining the software on your own servers, please submit an issue or pull request. The latest released version of Partek flow when this was written was: 6.0.17.0919.278-1 and serves as a start point for reference. It is possible that this module will work with prior partekflow versions; however, that condition has not been tested.

While the module maintainer supports the puppet code contained in the module, support for the application or performance of the Partek Flow software should be directed toward Partek. The module maintainer does not have a relationship with Partek.

Development

Please see the CONTRIBUTING document for information on how to get started developing code and submit a pull request for this module. While written in an opinionated fashion at the start, over time this can become less and less the case.

Contributors

To see who is involved with this module, see the GitHub list of contributors or the CONTRIBUTORS document.

millerjl1701 / millerjl1701-partekflow