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