Proteomics: ddl scripts + etl stored procedures

- Converted scripts from oracle version
Merge branch 'master' into improvements/proteomics_to_postgres
Add target to download transmart-loader
Target to download uniprot dictionary from remote server
Alternative target for downloading transmart-loader
Managing transmart-loader from transmart-data
Fix id collision

Increase searchapp index to start from
Add sample_dimension table

Converted from oracle
Add target to install maven
Change git protocol in favour to https

Aperently git protocol does not work for some servers
Fixes for maven calls
Make/Shell scripts for running proteomics etl
Proteomics stored procedures fixes
Make regexp_replace replace all occurences

Fix oracle vs postgresql regexp_replace function discrepancy
Split different samples to separate nodes
Regenerate result file if script has been changed
Replace dash from uniprotId to match with dictionary
Target to download transmart-data from Bamboo CIS

- moved log4j conf. file creation to env makefile
Add more error catching statements to sp

-Prevent transaction to be rolled back
Merge branch 'master' into improvements/proteomics_to_postgres

Conflicts:
	ddl/postgres/deapp/de_subject_protein_data.sql