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PhamDB: Make your own Phamerator databases

| posted 19 Oct, 2017 02:10
Hi all!

I am trying to use the SEA PHAGES vm to view PhamDB databases and I am having a bit of trouble.
I follow the instructions for adding the server and database listed by PhamDB but then I get that "password required error". At that point I have to reinstall the machine to get rid of this error and to view the Actino_draft database once again.
After reaading some of Chris' comments else where I had a go at using the PhamDB address in the web browser in the VM and that can be reached, just not by Phamerator. On the same lap top outside of the VM, I am also able to contact the site.

Any thoughts about what could be going wrong?

All best,

Heather
Edited 19 Oct, 2017 02:27
| posted 19 Oct, 2017 16:05
Hi Heather,

As long as everything is precisely typed into Phamerator, I think this is likely to be a Phamerator-Ubuntu issue rather than a PhamDB issue. Check out the suggestions in this post and see if any of those might help. Sometimes, weird stuff can happen on the VM which sends Phamerator into strange cycles, but Steve had a couple suggestions.

https://seaphages.org/forums/topic/246/?page=1#post-1338

–Dan
| posted 19 Oct, 2017 16:13
If you are getting the "Database setup required" window that looks like this.

you just need to enter the root database password "phage" (without the quotes) to authorize updating the system. If you are getting a different kind of password error box can you send the exact wording or a pic.
Edited 19 Oct, 2017 16:18
| posted 19 Oct, 2017 19:26
Woooooo hoooooooo! Whooooooooo Hooooooo! WHAHAHAHAHAHHHHHHAAAAAAAAAH!

Thanks guys, that 'phage' password worked. I am in heaven.

HH
| posted 20 May, 2020 12:43
hi,Dan, I have trouble with the creating database in the http://localhost, the create database button doesn't work, I cannot go to the next step, I have already uplouded the gb files, I donot know where is the problem, If you have any relevant solutions, please let me know, it will be my honor, looking forward to your reply, thanks a lot.
| posted 21 May, 2020 16:18
Database creation takes A LOT of computation and scales up exponentially with the number of phage.
Are you just working with 18 phage or did you add 18 phage to a larger database?
With 18 phage I would expect it to take at least a few minutes maybe up to 10, if you are adding phage to something larger it could take several hours to overnight. The last time I did this with ~100 phage on a pretty powerful computer it took over 2 hours.

The best way to get feedback and know if it is probably working is to use the utility in your OS that tells you how hard your CPU is working (either Activity Monitor on Mac or Task Manager in Win). If your phamdb is set up correctly, after you click the button you should see your CPU usage spike up and stay busy.
 
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