Running Hybrid Transeq (+UMI) Pipelines on LSF Suite

Owned by Rotem Barzilay
Last updated: Jul 13, 2020
2 min read

Introduction

The LSF Suite is a web app that integrates with our powerful grid, it is only exposed inside weizmann network.

It gives you a friendly graphic interface so you can easily run a pipeline on the grid and watch its progress.

We have 2 different Hybrid Transeq pipelines exposed in the LSF Suite:

  • Hybrid Transeq

  • Hybrid Transeq UMI

Pipelines Input

Hybrid Transeq - you need to create a folder in [your home folder]/data/[run name]/ and put there all your fastq’s

Hybrid Transeq UMI - you need to create a folder in [your home folder]/data/[run name]/ and put there the inside of the illumina run folder + a samplesheet file.

Pipelines Output

The output of the pipelines will be located in [your home folder]/projects/external_[username]_[date]/ which will have 2 or 3 sub folders:

  • [your home folder]/projects/external_[username]_[date]/demultiplexing/ (only with Hybrid Transeq UMI)

  • [your home folder]/projects/external_[username]_[date]/old-genome/

  • [your home folder]/projects/external_[username]_[date]/new-genome/

*For each sub folder, a log.txt file will exist, where you can see the progress of the step.

Running a Pipeline

  • Login to the web app using your incpm user and password: https://ilsf.incpm.weizmann.ac.il:8443/ (if you get a security warning, click “Advanced” and then “Proceed”)

  • Go to Workload → New Workload:

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  • Choose The “Pipelines” → “hybrid_transeq” folder and then you’ll see the 2 hybrid transeq pipelines:

     

  • Choose the requested pipeline and fill the “run name” parameter, then hit the “Submit” button to submit your pipeline:

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  • Then you will see the summery of the pipeline, where you can see the “Flow State”, it will finish with value “Done” if succeeded:

     

     

  • You can also change to the “Jobs“ tab, to see the progress of all the jobs it runs in the pipeline, when they all finish, the “Flow State” will change accordingly (you can refresh by moving tabs or hitting F5):