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NeatSeq-Flow-GUI Tutorial

In this Tutorial we will:

Install Conda

  • For Linux 64bit, in the terminal:

      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
  sh Miniconda2-latest-Linux-x86_64.sh

    During conda's installation: type yes to add conda to the PATH

    For different operating system go to Conda

Setup the Tutorial Work-Flow

  1. Create New Directory for the Tutorial 
      mkdir Tutorial
  cd Tutorial
  2. Download the NeatSeq Flow Tutorial installer file: 
      curl https://raw.githubusercontent.com/bioinfo-core-BGU/neatseq-flow-tutorial/master/NeatSeq_Flow_Tutorial_Install.yaml > NeatSeq_Flow_Tutorial_Install.yaml
  3. Create the NeatSeq_Flow_Tutorial conda environment: 
       conda env create -f NeatSeq_Flow_Tutorial_Install.yaml
  4. Download the Tutorial Work-Flow Parameter file 
       curl https://raw.githubusercontent.com/bioinfo-core-BGU/neatseq-flow-tutorial/master/Example_WF_conda_env.yaml > Tutorial_Parameter_file.yaml
  5. Download the Tutorial Work-Flow Sample file 
       curl https://raw.githubusercontent.com/bioinfo-core-BGU/neatseq-flow-tutorial/master/Samples_conda.nsfs > Tutorial_Samples_file.nsfs

Install NeatSeq-Flow

  1. Download the NeatSeq-Flow installer file: 
      curl https://raw.githubusercontent.com/bioinfo-core-BGU/NeatSeq-Flow-GUI/master/NeatSeq_Flow_GUI_installer.yaml > NeatSeq_Flow_installer.yaml
  2. Create the NeatSeq_Flow conda environment: 
      conda env create -f NeatSeq_Flow_installer.yaml
  3. Activate the NeatSeq_Flow conda environment: 
      bash
  source activate NeatSeq_Flow
  4. Run NeatSeq_Flow_GUI: 
      NeatSeq_Flow_GUI.py

Learn How to Create a Work-Flow

  1. Add New Step:

    In the 'Work-Flow' Tab choose a module template and click on the 'Create New Step' button.

  2. Change Step Name:

    You can change the new step name by clicking on the step name and edit the key field and then click the 'Edit' button to set the change.

  3. To determine the position of the new step in the work-flow:

    • Click on the step button to see the step options
    • Click on the base option
    • Click on the 'Value options' drop-down menu
    • Choose a previous step and click the 'Add' button. This can be repeated to choose several previous steps.
    • Click the 'Edit' button to set the changes.

  4. Add new step option:

    • Click on the step's name (or a step option to create a new sub option)
    • Click on the 'New' button.
    • It is possible to edit the new option name and value by editing the 'Key' field and the 'Value' field, it is also possible to choose from the 'Value options' drop-down menu.
    • Click the 'Edit' button to set the changes.

  5. Edit step's options:

    • Click on the step's option name and change the 'Key' field and/or the 'Value' field, it is also possible to choose from the 'Value options' drop-down menu.
    • When using the 'Value options' drop-down menu, in some cases it is possible to choose variables that are defined in the 'Vars' Tab. They will appear in the form of {Vars.some_field.some_sub_field} to indicate the value found in the 'Vars' Tab in the some_sub_field field ( which is a sub field of 'some_field' ).
    • It is possible to choose file location as a value to the 'Value' field by clicking on the 'Browse' button.
    • Click the 'Edit' button to set the changes.

  6. Duplicate field or step:

    • Click on the step's name (to duplicate the step) or on a step's option name (to duplicate the option and it's sub fields)
    • Click the 'Duplicate' button

  7. Remove field or step:

    • Click on the step's name (to remove the step) or on a step's option name (to remove the option and it's sub fields)
    • Click the 'Remove' button

Configure the Used Variables in the Work-Flow

  1. Edit Variables:

    In the 'Vars' Tab choose a variable name to edit, change the key or value and then click on the 'Edit' button.

  2. Create New Variable:

    • You can create new variable by clicking on some existing variable name and then click the 'New Field' button.
    • You can create new sub variable by clicking on the existing variable to which you want to create a sub variable and then click the 'New Sub Field' button.

Load a Work-Flow Parameter File

  1. Load a Parameter file:

    • In the 'Work-Flow' Tab click on the 'Load WorkFlow' button, then choose the work-flow's parameter file 'Tutorial_Parameter_file.yaml' and click open.

Configure a Sample file

In the 'Samples' Tab:

  1. Edit The Project Title Name:

    • You can edit the project title name by clicking on the Project Title name.

  2. Add a Sample/Project File:

    • You can add a sample/project file by clicking the 'Add Sample File' or 'Add project File' button and choose a file/s.

  3. Load a Sample file:

    • Click on the 'Load Sample File' button, then choose the work-flow's sample file 'Samples_conda.nsfs' and click open.

    • You can edit the names of the samples by clicking on the sample name.

    • You can remove a sample/project file by clicking the 'Remove' button.

    • You can change a sample/project file type by clicking the drop-down menu or by editing the type name.

Configure the Cluster information

  1. Edit Field:

    In the 'Cluster' Tab choose a field name to edit, change the key or value and then click on the 'Edit' button.

  2. Create New Field:

    • You can create new field by clicking on some existing field name and then click the 'New Field' button.
    • You can create new sub field by clicking on the existing field to which you want to create a sub field and then click the 'New Sub Field' button.

Run the Work-Flow

If NeatSeq-Flow is installed using conda (as in this Tutorial):

  • Choose the conda environment of which NeatSeq-Flow installed in.

If NeatSeq-Flow is installed Locally:

  • Choose the neatseq_flow.py script location.

In order to Generate the Work-Flow scripts:

  1. Select the Sample file.
  2. Select the Work-Flow parameter-file.
  3. Choose the Project Directory to generate the Work-Flow scripts in (the default is to use the Current Working Directory )
  4. Click on the 'Generate scripts' button.

To run the Work-Flow click on the 'Run scripts' button

It is possible to monitor the Work-Flow progress by clicking the 'Run Monitor' button

It is possible to terminate the current run by clicking on the 'Kill Run' button.

Contact

Please contact Liron Levin at: levinl@post.bgu.ac.il