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#Installation of tools

This chapter describes how to install the tools and reference data.

##Tools for imputation On BBMRI-NL VO of BigGrid and the cluster.gcc.rug.nl cluster all binaries needed are installed. To run the imputation pipeline on another server the following tools and scripts are required:

  • java
  • python
  • ChunkChromosome (v. 2012-08-28)
  • minimac (v. beta-2012.10.3) [^3]
  • mach (v. 1.0.18) [^6]
  • plink (v. 1.07)
  • plink1.08 (v. 1.08)
  • imputationTool (v. 20120912)
  • ConcatWorksheets (v. V1.0)
  • expandWorksheet (v. V1.1)
    Note1: Version numbers are tested
    Note2: Download links can be found in chapter 9 "Appendix""

We recommend to install all tools in one directory in a structure of tools//, this way only the "$tooldir" variable in the parameters.csv needs to be changed.

##Tools for NGS
On BBMRI-NL VO of BigGrid and the cluster.gcc.rug.nl cluster all binaries needed are installed.

To run the NGS pipeline elsehwhere one should first install all needed tools. We recommend to setup a directory $root directory which contains the following folders; tools/ and resources. The following tools should be installed in the tool/ directory:

Tools Downloadlink
GATK http://www.bbmriwiki.nl/svn/ebiogrid/modules/GATK/1.0.5069/GATK-1.0.5069.tgz
BWA http://www.bbmriwiki.nl/svn/ebiogrid/modules/bwa/0.5.8c_patched/bwa-0.5.8c_patched.tgz
fastQC http://www.bbmriwiki.nl/svn/ebiogrid/modules/fastqc/v0.10.1/fastqc-v0.10.1.tgz
picard-tools http://www.bbmriwiki.nl/svn/ebiogrid/modules/picard-tools/1.61/picard-tools-1.61.tgz

Scripts should be downloaded in installed in tools/scripts/. All scripts can be downloaded here:

script Downloadlink
coverage.R http://www.bbmriwiki.nl/svn/ebiogrid/scripts/coverage.R
createInsertSizePlot http://www.bbmriwiki.nl/svn/ebiogrid/scripts/createInsertSizePlot.zip
filterSingleSampleCalls.pl http://www.bbmriwiki.nl/svn/ebiogrid/scripts/filterSingleSampleCalls.pl
plot_cumulative_coverage http://www.bbmriwiki.nl/svn/ebiogrid/scripts/plot_cumulative_coverage-1.1.R

All resources can be downloaded here: insert_link
After extracting the resources one can just move the resources/ directory onder the $root since they are packed in the correct folder structure.

After installing all tools and resources one should have the following directory structure:

    -root  
      |
      +tools
      |   |
      |   +scripts
      |   |   <analysis scripts>
      |   |
      |   +<several tools, one tool per folder> SEE: Note 1
      |  
      +resources
           |
           +hg19
              |
              +dbsnp
              |   <dbsnp files>
              |
              +indels
              |   <indel files (VCF)>
              |
              +indices
              |   <human_g1k_v37.fa files>
              |
              +intervals
                  <interval_list files>  
                  
    Note:  
    1 These tools are the ones described above  
    2 When using the grid as described in chapter 4 all tools are installed and usable as `module`.