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Toolbox for generic NGS analyses

Development Manual

If you want to add a new tool, TOGGLe will automatically help you to integrate it.

addingNewSoft.pl creates a fonction, a module and a block if they do not exist. It can also add a new fonction into an already existing module.

Launch addingNewSoft.pl and answer the following questions:

  • Choose a module and a fonction name for your tool. Here an exemple to integrate bwa :
What is the name of your tool (e.g. bwa) ?
What is the name of your function (e.g. bwaAln for bwa aln) ?
  • You have to know input formats …
What are the different entry formats of your tool, separated by commas (e.g. fastq or fastq,fasta) ?
  • … and the tool output formats
What are the different output formats of your tool, separated by commas (e.g. fastq or fastq,fasta) ?
NOTE if your tool is a dead-end one, such as FASTQC, please provide NA as output format
  • Some tools have requirements, this requirements will be add in a softwareManagement.pm
Are there any mandatory requirement as option for your tool (e.g. reference or gff) ?
NOTE if none leave empty;
  • You have to give the command line to obtain tool version
How do you obtain the version of your tool (e.g. 'bwa 2>&1| grep version' or 'java --version | grep Version')
  • Now we are testing if the command version is ok. The testParams value will be used in the fileConfigurator.pm module for block test
Are there any test parameters to include for testing (e.g. '-n 5' for bwa aln tests ) ?";
What is the standard command line to launch your tool ?
    A file in must be written FILEIN
    A file out must be written FILEOUT
    Options location must be written as [options]
    Reference must be written as REFERENCE
    Gff/Gtf must be written as GFF
    Keyfile must be written as KEYFILE
    Vcf must be written as VCF;
An example for bwa aln will be: bwa aln [options] FILEOUT REFERENCE FILEIN;
NOTE You may have to adapt and correct this command at this end...;
  • addingNewSoft.pl helps you to integrate a new tool but it does not everything!. You have to look at the following files to check if everything is Ok:
- modules/$moduleFile NOTE: Please check if the variable is noted as $bwa and not /usr/bin/bwa !!
- modules/localConfig.pm
- modules/softwareManagement.pm NOTE: Please check if the variable is noted as $bwa and not /usr/bin/bwa !!
- modules/fileConfigurator.pm NOTE: Please add line $function =>[\"\"] to add default value for test block
    - onTheFly/$blockName
    - test/modules/$moduleTest
    - dont forget to add use $module in startBlock.txt message
    - test/blocks/$blockTest
  • For more details about syntax, modules, blocks and test builiding please check the DevManual4Toggle.pdf
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