central-decider-client

This tool is used to generate workflow.ini files. It takes in a list of donors or samples from a whitelist, queries the central decider and then generates an INI file for each of the samples in the provided list. Information in the resulting INI's come from either the INI template or from information provided by the central decider.

##Author Adam Wright (adam.j.wright82@gmail.com)

##Steps to get started:

1. Obtain password from OICR, email Adam
2. Obtain Whitelist of donors or samples from OICR, email Christina Yung Christina.Yung@oicr.on.ca for a list and see them stored here: https://github.com/ICGC-TCGA-PanCancer/pcawg-operations
3. Clone this repository into desired location
4. Install required packages
5. Generate INI's through providing generate_ini_files.pl with the desired input through command line flags
6. Ini files will appear in the ini folder after being generated

*by default, INI files that have been previously run and submitted to a PanCancer GNOS repository will not be generated.

##Example Command perl generate_ini_files.pl --workflow-name=SangerPancancerCgpCnIndelSnvStr --gnos-repo=https://gtrepo-ebi.annailabs.com/ --whitelist=whitelist-ebi.txt --test --template-file=templates/dkfz-embl-template.ini --password= --vm-location-code=ebi

##Example transfer to S3 perl generate_ini_files.pl --test --workflow-name=Workflow_GNOS_to_S3 --password= --vm-location-code=bsc --template-file=templates/gnos_to_s3.ini --number-of-donors=1

##Workflow names that the central decider creates INI's for

  [vcf]
  SangerPancancerCgpCnIndelSnvStr=sanger
  DEWrapperWorkflow=german
  DKFZWorkflow=german
  EMBLWorkflow=german

  [bam]
  Workflow_Bundle_BWA=bwa

  [transfer]
  Workflow_GNOS_to_S3=s3

##Environment This tool is designed and tested with a Ubuntu 14.04 environment. The tool requires minimal CPU and memory. As the client performs a http request to the central decider the machine will require internet access on port 80.

##Password In order to use this tool you will need a password. This password is used by the decider client when making a get request to the central decider. Although the INI files do not contain sensitive information, requiring authentication prevents malicious querying of the central decider / elasticsearch database.

##Installation If you have cpanminus run: cpanm --quiet --notest --installdeps .

  Or with Apt-get run: sudo apt-get update; sudo apt-get install make git libipc-system-simple-perl libgetopt-euclid-perl libjson-perl libwww-perl libdata-dumper-simple-perl libtemplate-perl 

##DKFZ / EMBL Workflows In order to specify the correct parameters and to schedule out the German Workflows refer to: https://github.com/ICGC-TCGA-PanCancer/DEWrapperWorkflow#user-tips-for-workflow-settings

##Creating Template Within the template folder there are samples templates for each of the major workflows that we run with the PanCancer project. With in these templates there are are values that can get injected into the templatem, when generating the INI files.

The the fields that get injected will appear in template in the format "[% <desired-field-name> %]", where you wil replace "<desired-field-name>" with one of the following values:

field name	Example Injected Value
upload_gnos_key	TCGA
control_analysis_id	1f3cb1fe-a83f-4099-b4d4-0f0f6a3c0e48
tumour_analysis_ids	88545635-e0dd-4710-a762-fb8bf1408d23
workflow_name	SangerPancancerCgpCnIndelSnvStr
control_bam	PCAWG.458023b4-e6d6-45d4-bebe-2321fc693837.bam
tumour_bams	PCAWG.fe319028-03ac-4741-bcc2-a6ed7a1e07ce.bam
vm-location-code	ebi
project_code	UCEC-US
tumour_aliquot_ids	31bc44b9-35ff-43fd-8a01-a834f3b1ce46
download_gnos_url	https://cghub.ucsc.edu/
upload_gnos_url	https://gtrepo-osdc-tcga.annailabs.com/
donor_id	f6d136c7-c250-4361-9fed-50f513959a40
download_gnos_key	cghub

##Command line flags

see generate_ini_files.pod

##Travis

Travis utility is used to test if the repo is compiling correctly