| Description | Hands On Lab Exercises for TOGGLe |
|---|---|
| Related-course materials | TOGGLe introduction |
| Authors | Sébastien RAVEL (sebastien.ravel@cirad.fr) Christine TRANCHANT (christine.tranchant@ird.fr) |
| Creation Date | 15/03/2018 |
| Last Modified Date | 16/04/2019 |
Summary
Creating your own workflow :
Practice 1 consists of using base one pre-defined configuration file to build own workflow to use with TOGGLe.
The SNPdiscoveryPaired.config.txt file is an example of how to customize your pipeline.
Providing an order
The order of a pipeline is provided with key $order, base on the file, build new config file to run only from mapping to SNP calling.
TP on IRD cluster
All input data:
- Input data : /data2/formation/TPsnpSV/fastqDir/
- Reference : /data2/formation/TPsnpSV/reference.fasta
- Config file: /data2/formation/TPsnpSV/configFiles/SNPdiscoveryPaired.config.txt
To do:
- Create a “formationX” directory in your account
- Make à copy for reference and input data into “formationX” directory (scp).
- Add the configuration file used by TOGGLe and change SGE key as below
$sge
-q formation.q
-b Y
-cwdConnect to account and prepare datas:
- Connect to the cluster:
ssh -Y formationX@bioinfo-master.ird.fr- Launch a QRSH command:
qrsh -q formation.q- Transfer the data from nas using SCP:
scp -r nas:/data2/formation/TPsnpSV .- Load TOGGLe tools:
module load bioinfo/TOGGLE/0.3.6Launching an analysis
Use only one script to run all pipeline: toggleGenerator.pl script usage
toggleGenerator.pl -d|--directory DIR -c|--config FILE -o|--outputdir DIR [-r|--reference FILE] [-k|--keyfile FILE] [-g|--gff FILE] [-nocheck|--nocheckFastq] [--help|-h]| Required named arguments: | |
|---|---|
| -d / –directory DIR: | a folder with raw data to be treated (FASTQ, FASTQ.GZ, SAM, BAM, VCF) |
| -c / –config FILE: | generally it is the software.config.txt file but it can be any text file structured as shown below. |
| -o / –outputdir DIR: | the current version of TOGGLE will not modify the initial data folder but will create an output directory with all analyses in. |
| Optional named arguments: | |
|---|---|
| -r / –reference FILE: | the reference FASTA file to be used. (1) |
| -g / -gff FILE: | the GFF file to be used for some tools. |
| -k / –keyfile FILE: | the keyfile use for demultiplexing step. |
| -nocheck / –nocheckFastq: | by default toggle checks if fastq format is correct in every file. This option allows to skip this step. |
| -report / –report: | generate pdf report (more info) |
| -h / –help: | show help message and exit |
(1): If no database index exists, it will be automatically created if it is necessary. If the index already exists, they will not be re-created UNLESS the pipeline order (see below) expressively requests it (updating the index e.g.)
All the the paths (files and folders) can be provided as absolute (/home/mylogin/data/myRef.fasta) or relative (../data/myRef.fasta).
Example of a command to run TOGGLe :
toggleGenerator.pl -d ~/toggle/fastq -c ~/toggle/SNPdiscoveryPaired.config.txt -o ~/toggle/outputRES -r ~/toggle/reference.fasta -nocheck -reportSOLUTIONS:
vim SNPdiscoveryPaired.config.txt
qsub -q formation.q -b Y -N TOGGLE "module load bioinfo/TOGGLE/0.3.6; toggleGenerator.pl -c /home/formationX/TPsnpSV/configFiles/SNPdiscoveryPaired.config.txt -d /home/formationX/TPsnpSV/fastqDir/ -r /home/formationX/TPsnpSV/reference.fasta -o /home/formationX/outputTOGGLe -nocheck -report"Links
- Related courses : TOGGLe
License
