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You don't say what OS environment or CPU architecture your server has.
But back in the day when I did FPGA development at work, we had Quartus tools installed on linux PC servers on the network.
We could use Xwindows on our PCs to interface to Quartus graphical tools, just like you would on a Windows PC.
Or we could ssh into the server and run the tools in command line mode as scripts.
In fact most times I run Quartus now I do it thru a cygwin command line environment on my PC.
Just go to the design root and type 'make' and all the appropriate tools get run in the order required.
I very rarely go into the graphical environment any more.
So if you have an X86 Linux server just go an install the Linux version of Quartus on it.
Here is a sample Makefile I use to control Quartus:
DESIGN=my_design all:: full full:: compile timing programming report part:: update programming compile:: $(QUARTUS_BIN)/quartus_map $(DESIGN) --write_settings_files=off $(QUARTUS_BIN)/quartus_fit $(DESIGN) --write_settings_files=off $(QUARTUS_BIN)/quartus_asm $(DESIGN) --write_settings_files=off update:: $(QUARTUS_BIN)/quartus_cdb $(DESIGN) --write_settings_files=off --update_mif $(QUARTUS_BIN)/quartus_asm $(DESIGN) --write_settings_files=off timing:: $(QUARTUS_BIN)/quartus_sta $(DESIGN) $(QUARTUS_BIN)/quartus_sta -t generate_timing.tcl $(DESIGN) 10 $(QUARTUS_BIN)/quartus_eda $(DESIGN) --write_settings_files=off -c $(DESIGN) programming:: $(QUARTUS_BIN)/quartus_cpf -c $(DESIGN).cof report:: @-echo ' ' -egrep --color -i '\([0-9]+ violated\)' TQ_*.rpt @-echo ' ' -egrep -vi '^this panel reports' TQ_fmax_summary.rpt @-echo ' ' clean:: -rm -f $(DESIGN).*.rpt $(DESIGN).*.summary $(DESIGN).*.smsg $(DESIGN).map -rm -f $(DESIGN)_assignment_defaults.qdf TQ_*.rpt PLL*.txt meminit.txt -rm -f $(DESIGN).done $(DESIGN).map $(DESIGN).pof $(DESIGN).sof $(DESIGN).jic -rm -f $(DESIGN).pin $(DESIGN).jdi $(DESIGN).qws $(DESIGN).*.ddb $(DESIGN).sld -rm -rf db incremental_db simulation # the end