MOLGENIS Pipelines
  • Introduction
  • Release Notes
  • Environment setup with easybuild
    • Install environment
  • NGS_DNA
  • NGS_RNA
    • Install pipeline
    • Dependencies
    • Run
    • Workflow
    • Protocols
  • MOLGENIS Compute
    • Quickstart
    • Parameters
    • Reference
    • Read more
  • MOLGENIS CoNVaDING
    • CoNVaDING
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  • 1) Installing NGS_RNA
  • 2) Installing the necessary resources (reference genome, dbSNP etc)
  • 3) Creating workdir structure
  1. NGS_RNA

Install pipeline

PreviousNGS_RNANextDependencies

Last updated 6 years ago

1) Installing NGS_RNA

We first have to load EasyBuild, this can be done with this command

module load EasyBuild

The NGS_RNA pipeline has a lot of dependencies, these are handled by easybuild when the --robot command is executed (all the dependencies can be found ). Since we have also our own repo we have to give the path to that also. There can be multiple paths to easybuild configs, just separate them by colon.

Note: the order in which you give the paths are important! To original easybuild path can be left empty (just a colon is enough)

eb NGS_RNA-3.2.4.eb --robot --robot-paths=${pathToMYeasybuild}/easybuild-easyconfigs/easybuild/easyconfigs/:

Note: some software cannot be downloaded automagically due to for example licensing or technical issues and the build will fail initially. In these cases you will have to download manually and copy the sources to ${HPC_ENV_PREFIX}/sources/[a-z]/NameOfTheSoftwarePackage/ This is the case for example for Java. Therefore:

scp jdk-7u80-linux-x64.tar.gz your_account@yourcluster.nl:${root}/apps/sources/j/Java/
scp jdk-8u45-linux-x64.tar.gz your_account@yourcluster.nl:${root}/apps/sources/j/Java/

but also tools as GATK, Tabix and snpEff should be download manually:

scp GATK-3.5.tar.gz your_account@yourcluster.nl: ${root}/apps/sources/g/GATK/
scp tabix.0.18.6.tar.gz your_account@yourcluster.nl: ${root}/apps/sources/t/tabix

2) Installing the necessary resources (reference genome, dbSNP etc)

Logout and login again. Run the script RNA_resources to install the required resources, you can download the scripts 

sh NGS_RNA-resources.sh

This script will download parts of the 2.8 bundle from the GATK server

Note: Sometimes the GATK ftp server can be down/instable, try it a couple of times

3) Creating workdir structure

sh makestructure.sh
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