SGT handling function is not being called in pgdac_harmonize

[ramanibk]

• process.duplicate.genes was the original function for rolling genes with "maxvar" as the default policy.
• A new R function process.duplicate.genes.2 was created and stored in the script process_duplicate_genes.r. This script lies inside proteomics-Rutil repository and sources pgdac_ptmsea_functions.R.
• Parameters to indicate that the desired policy is 'SGT' were passed through additional_parameters which would then get appended to the config.r.
• However, harmonize.r does not call process.duplicate.genes.2 and still calls process.duplicate.genes.

NOTE: branch to fix this bug should be called bug-1

[ramanibk]

harmonize.r now calls process.duplicate.genes.2 for handling gene roll up.

• Changed data.matrix function in harmonize.r to data.matrix.harmonize to avoid conflict with base function called in pgdac_ptmsea_functions.R
• harmonize.r now checks if pome.duplicate.gene.policy exists. If it does not, the script creates that variable and sets it to the duplicate.gene.policy variable value (which by default is set to maxvar)
• harmonize.r checks if policy is SGT. If it is, the script then adds subgroupNum to the rdesc columns
• process_duplicate_genes.r calls process.duplicate.genes (the original one) from within process.duplciate.genes.2 if policy is either mean, maxvar, or median.

Other Changes:

• setup.sh now adds latest tag to every docker that gets built along with the original commit hash tag. To clarify, every docker that gets built will have two tags:
  • most recent six-character git commit hash
  • latest
• setup.sh pushes both the tags to Dockerhub
• There will be only one latest tag for each docker_namespace/docker_name and will point to the most recent docker added to Dockerhub
• All Dockerfiles and WDLs now have broadcptacdev/docker_name:latest for docker references
• update.sh NO longer has the code that:
  • interacts with the docker API to get the most recent docker tag for each parent docker
  • updates child Dockerfile with the retrieved most-recent tag for its parent docker
• update.sh no longer builds and pushes the docker whose children need to be updated